external authentication - empty REMOTE_USER
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: <?PHP foreach($_SERVER as $key_name => $key_value) { print $key_name . " = " . $key_value . "<br>"; } ?> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value. I don't understand where my problem lies. Here is my galaxy.conf file : Listen 2208 <VirtualHost *:2208> RewriteEngine on DocumentRoot "/path/to/static" <Directory "/path/to/static"> Options +Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny Allow from all AuthType Basic AuthName "Authentifiez vous" PerlAuthenHandler Apache2::AuthenNIS PerlAuthzHandler Apache2::AuthzNIS PerlSetVar AllowAlternateAuth no require valid-user </Directory> RewriteEngine on RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e RewriteRule ^/galaxy$ /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$1 [P] </VirtualHost> Thanks in advance ! F.T
I just recently submitted a patch that will display all the environment variables being passed to Galaxy in pastor.log. That should help you determine if the variables are set and to what. Please excuse any typos -- Sent from my iPhone
On Oct 21, 2015, at 6:11 AM, Floreline TOUCHARD <floreline.touchard@gmail.com> wrote:
Hi,
I've got an issue with my external authentication configuration. I use Apache and the mod_perl
modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS accounts.
I have the authentication form when I try to access galaxy web page. But after a successful authentication it seems that the REMOTE_USER variable is not passed to my galaxy instance. I'm connected under "@example.org" regardless of the authentication account. That's why I think the REMOTE_USER passed to Galaxy is not 'null' but empty.
I tested the value of the variable with the following php script:
<?PHP foreach($_SERVER as $key_name => $key_value) { print $key_name . " = " . $key_value . "<br>";
}
?>
I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
I don't understand where my problem lies.
Here is my galaxy.conf file :
Listen 2208
<VirtualHost *:2208>
RewriteEngine on DocumentRoot "/path/to/static"
<Directory "/path/to/static">
Options +Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny Allow from all
AuthType Basic AuthName "Authentifiez vous" PerlAuthenHandler Apache2::AuthenNIS PerlAuthzHandler Apache2::AuthzNIS PerlSetVar AllowAlternateAuth no require valid-user
</Directory>
RewriteEngine on RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e
RewriteRule ^/galaxy$ /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$1 [P]
</VirtualHost>
Thanks in advance !
F.T
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Thank you ! Can you tell me which files are to update or download ? I installed my application on a server that was not open to the outside. Currently I do not support different versions or updates of my application with git. I can download the files to edit and transfer them to the server but not to update the entire application at the moment. F. T Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" <floreline.touchard@gmail.com> a écrit :
Hi,
I've got an issue with my external authentication configuration. I use Apache and the mod_perl
modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS accounts.
I have the authentication form when I try to access galaxy web page. But after a successful authentication it seems that the REMOTE_USER variable is not passed to my galaxy instance. I'm connected under "@ example.org" regardless of the authentication account. That's why I think the REMOTE_USER passed to Galaxy is not 'null' but empty.
I tested the value of the variable with the following php script:
<?PHP foreach($_SERVER as $key_name => $key_value) { print $key_name . " = " . $key_value . "<br>";
}
?>
I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
I don't understand where my problem lies.
Here is my galaxy.conf file :
Listen 2208
<VirtualHost *:2208>
RewriteEngine on DocumentRoot "/path/to/static"
<Directory "/path/to/static">
Options +Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny Allow from all
AuthType Basic AuthName "Authentifiez vous" PerlAuthenHandler Apache2::AuthenNIS PerlAuthzHandler Apache2::AuthzNIS PerlSetVar AllowAlternateAuth no require valid-user
</Directory>
RewriteEngine on RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e
RewriteRule ^/galaxy$ /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$1 [P]
</VirtualHost>
Thanks in advance !
F.T
Hi Floreline, The files from Ryan's pull request are visible here: https://github.com/galaxyproject/galaxy/pull/823/files It's a pretty simple change to enable some extra debugging information that might help you discover the cause of your issue. On 10/21/2015 07:40 AM, Floreline TOUCHARD wrote:
Thank you ! Can you tell me which files are to update or download ? I installed my application on a server that was not open to the outside. Currently I do not support different versions or updates of my application with git. I can download the files to edit and transfer them to the server but not to update the entire application at the moment.
F. T
Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" <floreline.touchard@gmail.com <mailto:floreline.touchard@gmail.com>> a écrit :
Hi,
I've got an issue with my external authentication configuration. I use Apache and the mod_perl
modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS accounts.
I have the authentication form when I try to access galaxy web page. But after a successful authentication it seems that the REMOTE_USER variable is not passed to my galaxy instance. I'm connected under "@example.org <http://example.org>" regardless of the authentication account. That's why I think the REMOTE_USER passed to Galaxy is not 'null' but empty.
I tested the value of the variable with the following php script:
<?PHP foreach($_SERVER as $key_name => $key_value) { print $key_name . " = " . $key_value . "<br>";
}
?>
I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
I don't understand where my problem lies.
Here is my galaxy.conf file :
Listen 2208
<VirtualHost *:2208>
RewriteEngine on DocumentRoot "/path/to/static"
<Directory "/path/to/static">
Options +Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny Allow from all
AuthType Basic AuthName "Authentifiez vous" PerlAuthenHandler Apache2::AuthenNIS PerlAuthzHandler Apache2::AuthzNIS PerlSetVar AllowAlternateAuth no require valid-user
</Directory>
RewriteEngine on RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e
RewriteRule ^/galaxy$ /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$1 [P]
</VirtualHost>
Thanks in advance !
F.T
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Ciao, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
Here is the pull request: https://github.com/galaxyproject/galaxy/pull/823 You can see what file was edited On Wed, Oct 21, 2015 at 8:40 AM, Floreline TOUCHARD < floreline.touchard@gmail.com> wrote:
Thank you ! Can you tell me which files are to update or download ? I installed my application on a server that was not open to the outside. Currently I do not support different versions or updates of my application with git. I can download the files to edit and transfer them to the server but not to update the entire application at the moment.
F. T Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" < floreline.touchard@gmail.com> a écrit :
Hi,
I've got an issue with my external authentication configuration. I use Apache and the mod_perl
modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS accounts.
I have the authentication form when I try to access galaxy web page. But after a successful authentication it seems that the REMOTE_USER variable is not passed to my galaxy instance. I'm connected under "@ example.org" regardless of the authentication account. That's why I think the REMOTE_USER passed to Galaxy is not 'null' but empty.
I tested the value of the variable with the following php script:
<?PHP foreach($_SERVER as $key_name => $key_value) { print $key_name . " = " . $key_value . "<br>";
}
?>
I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
I don't understand where my problem lies.
Here is my galaxy.conf file :
Listen 2208
<VirtualHost *:2208>
RewriteEngine on DocumentRoot "/path/to/static"
<Directory "/path/to/static">
Options +Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny Allow from all
AuthType Basic AuthName "Authentifiez vous" PerlAuthenHandler Apache2::AuthenNIS PerlAuthzHandler Apache2::AuthzNIS PerlSetVar AllowAlternateAuth no require valid-user
</Directory>
RewriteEngine on RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e
RewriteRule ^/galaxy$ /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$1 [P]
</VirtualHost>
Thanks in advance !
F.T
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Hi, thanks for the quick reply ! I did edit the remoteuser.py file and started the daemon again, but there's no change in the output in paster.log. Am I missing something ? F.T 2015-10-21 12:11 GMT+02:00 Floreline TOUCHARD <floreline.touchard@gmail.com> :
Hi,
I've got an issue with my external authentication configuration. I use Apache and the mod_perl
modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS accounts.
I have the authentication form when I try to access galaxy web page. But after a successful authentication it seems that the REMOTE_USER variable is not passed to my galaxy instance. I'm connected under "@ example.org" regardless of the authentication account. That's why I think the REMOTE_USER passed to Galaxy is not 'null' but empty.
I tested the value of the variable with the following php script:
<?PHP foreach($_SERVER as $key_name => $key_value) { print $key_name . " = " . $key_value . "<br>";
}
?>
I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
I don't understand where my problem lies.
Here is my galaxy.conf file :
Listen 2208
<VirtualHost *:2208>
RewriteEngine on DocumentRoot "/path/to/static"
<Directory "/path/to/static">
Options +Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny Allow from all
AuthType Basic AuthName "Authentifiez vous" PerlAuthenHandler Apache2::AuthenNIS PerlAuthzHandler Apache2::AuthzNIS PerlSetVar AllowAlternateAuth no require valid-user
</Directory>
RewriteEngine on RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e
RewriteRule ^/galaxy$ /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$1 [P]
</VirtualHost>
Thanks in advance !
F.T
Hi, here is some additional information : - I have no change in my paster.log with my current galaxy.conf file. - If I force the connexion with a user (with a RequestHeader set REMOTE_USER "<username>" in galaxy.conf), it works. My galaxy instance open on my user session, and I get a "galaxy.web.framework.webapp WARNING 2015-10-22 10:37:19,762 User logged in as '<username>@example.fr' externally, but has a cookie as '@example.fr' invalidating session" in the paster.log. Is it a syntax problem in my galaxy.conf file ? F.T 2015-10-21 12:11 GMT+02:00 Floreline TOUCHARD <floreline.touchard@gmail.com> :
Hi,
I've got an issue with my external authentication configuration. I use Apache and the mod_perl
modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS accounts.
I have the authentication form when I try to access galaxy web page. But after a successful authentication it seems that the REMOTE_USER variable is not passed to my galaxy instance. I'm connected under "@ example.org" regardless of the authentication account. That's why I think the REMOTE_USER passed to Galaxy is not 'null' but empty.
I tested the value of the variable with the following php script:
<?PHP foreach($_SERVER as $key_name => $key_value) { print $key_name . " = " . $key_value . "<br>";
}
?>
I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
I don't understand where my problem lies.
Here is my galaxy.conf file :
Listen 2208
<VirtualHost *:2208>
RewriteEngine on DocumentRoot "/path/to/static"
<Directory "/path/to/static">
Options +Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny Allow from all
AuthType Basic AuthName "Authentifiez vous" PerlAuthenHandler Apache2::AuthenNIS PerlAuthzHandler Apache2::AuthzNIS PerlSetVar AllowAlternateAuth no require valid-user
</Directory>
RewriteEngine on RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e
RewriteRule ^/galaxy$ /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]
</VirtualHost>
Thanks in advance !
F.T
participants (3)
-
Eric Rasche -
Floreline TOUCHARD -
Ryan G