On Jun 20, 2011, at 2:40 PM, Nate Coraor wrote: Thanks for the reply Nate. That's helpful. -- Shantanu.

Shantanu Pavgi wrote: Hi Shantanu, These should be sufficient and would not give access to anything job or tool related. However, since /datasets/ is exposed, this means that any dataset with no roles associated with the access permission (i.e. a "public" dataset) would be readable by anyone. Dataset IDs are encoded so as not to be easily guessable, but relying on this is essentially "security by obscurity." This cannot be done from within Galaxy, but it shouldn't be necessary since these actions are not exposed to the anonymous user. --nate

Leandro Hermida wrote: Hi Leandro, See the optional 'env=' argument and docs on the same for ways to make RequestHeader conditional: http://httpd.apache.org/docs/current/mod/mod_headers.html#requestheader So, depending on the path accessed, you should be able to have mod_rewrite set an environment variable specifying which REMOTE_USER (real username or fake anonymouse user) should be set. You could also just set it as the anonymous user to start with and then use 'RequestHeader set' to overwrite it with the real username in the case that a real username is available. This is all just from glancing at the docs, though, I have not tried any of it out, and this sort of Apache trickery is always difficult to get right. --nate

On Jun 28, 2011, at 2:15 PM, Nate Coraor wrote: Shantanu Pavgi wrote: I did a test by excluding following URLs from Apache-Shibboleth external authentication and it seems to be working: - /datasets/ - /u/<username>/h/<history-name> - /static/ (css and javascript) Do I need to exclude any other URLs so that published histories and datasets can be accessed from remote sites without authentication? Also, will it offer read-only access to the galaxy interface? Does it expose any job submission, file-uploads or any other modification/execution operations using web interface? Hi Shantanu, These should be sufficient and would not give access to anything job or tool related. However, since /datasets/ is exposed, this means that any dataset with no roles associated with the access permission (i.e. a "public" dataset) would be readable by anyone. Dataset IDs are encoded so as not to be easily guessable, but relying on this is essentially "security by obscurity." Thanks for the reply Nate. We are able to view datasets over to UCSC site if we directly append /dataset URL as a query parameter to the main UCSC URL. But we discovered one more use case where datasets contained in a particular history have a different URL format for UCSC link. For example, you should be able to access following URL without authentication: https://galaxy.uabgrid.uab.edu/history/list_shared?sort=-update_time&... Now if you click on dataset-1 and then click on 'display at UCSC main' then the resulting URL is as follows: https://galaxy.uabgrid.uab.edu/datasets/3423/display_at/ucsc_main?redirec... This link fails without authentication as we have exposed only /datasets URL pattern. I can manually insert /dataset URL for UCSC 'display_url', however it's not intuitive for end users. I am bit concerned about opening up "/root/display_as" URL pattern without knowing it's implications. I guess it doesn't expose any jobs or tools related access, but not sure about it. Any comments or suggestions? Also, can we prevent particular galaxy-user from carrying out certain actions, e.g. running jobs, file uploads etc.? Since galaxy will create 'anonymous' user account based on the REMOTE_USER variable set for unauthenticated requests, I am wondering if such locked-down mode will be possible for a particular galaxy-user. This cannot be done from within Galaxy, but it shouldn't be necessary since these actions are not exposed to the anonymous user. I think the user is not anonymous here as we have already written REMOTE_USER to 'anonymous' now. The galaxy receives this user as user-login/email as 'anonymous@mail.domain<mailto:'anonymous@mail.domain>'. Now we are opening up certain URL patterns to be accessed as 'anonymous@mail.domain<mailto:'anonymous@mail.domain>' user. These URL patterns include following formats as mentioned - /datasets, /history, /u/<username>/h<history-name>, and /static. In addition we may need to expose "/root/display_as" URL pattern as well. Rest of the site remains protected using real authentication. So as long as above URL patterns don't expose any job submission, file uploads or other galaxy tools operations then we should be OK with it. Thoughts? -- Thanks, Shantanu.

Shantanu Pavgi wrote: display_as is covered under "Display at UCSC": https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy You can expose it just to UCSC or globally. Since you're already exposing /datasets/ globally, doing the same with /root/display_as is probably not much different. --nate

On Jun 30, 2011, at 6:34 AM, Leandro Hermida wrote: Leandro, I realized that above mentioned configuration is wrong. It will set RequestHeader to 'anonymous' regardless of authentication status. I think following config should work (still testing). In our case it resides outside of Location directive now. You may need to adjust it according to your setup: {{{ # Take the environment variable and set it as a header in the proxy request. RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] # Set RU to anonymous if No REMOTE_USER RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} ="" RewriteRule . - [E=RU:"anonymous"] # Set RequestHeader RequestHeader set REMOTE_USER %{RU}e }}} -- Shantanu.

Hi again, I just realized that my setup is not going to work at all and does that exact thing you just mentioned, even if you are logged in it will set the REMOTE_USER to anonymous when you click on any /datasets URL. This causes some strange Galaxy history behavior! oops, Leandro On Fri, Jul 1, 2011 at 10:36 AM, Leandro Hermida <softdev(a)leandrohermida.com > Hi Shantanu, > > Thank you for your update, I've done my config a little differently and it > appears to work just the same. The relevant part looks like this: > > <Location /> > ## ActiveDirectory authentication and authorization > AuthType Basic > AuthBasicProvider ldap > AuthName "R&D Galaxy Testing/QA Server" > AuthLDAPURL "ldap://my.server.com:389/OU=Users & > Workstations,DC=domain,DC=com?sAMAccountName?sub?(|(objectClass=person)(objectClass=group))" > > # ...more AuthLDAP directives here... > > RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e > </Location> > > <Location /datasets> > Order Allow,Deny > Allow from All > Satisfy Any > > RequestHeader set REMOTE_USER "anonymous" > </Location> > > ## Static content and reverse proxy > RewriteEngine On > RewriteRule ^/static/style/(.*) > /path/to/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L] > RewriteRule ^/static/scripts/(.*) > /path/to/galaxy/galaxy_dist/static/scripts/packed/$1 [L] > RewriteRule ^/static/(.*) /path/to/galaxy/galaxy_dist/static/$1 [L] > RewriteRule ^/favicon.ico /path/to/galaxy/galaxy_dist/static/favicon.ico > [L] > RewriteRule ^/robots.txt /path/to/galaxy/galaxy_dist/static/robots.txt > [L] > RewriteRule ^(.*) http://galaxy.server.hostname:8080 [P] > > > > > On Fri, Jul 1, 2011 at 12:13 AM, Shantanu Pavgi <pavgi(a)uab.edu> > > > On Jun 30, 2011, at 6:34 AM, Leandro Hermida wrote: > > > >> Hi Nate and Shantanu, > >> > >> Thanks so much for the clear guidance, this works and sorry I didn't > >> read the Apache docs properly > >> > >> best, > >> Leandro > >> > >> On Thu, Jun 30, 2011 at 6:14 AM, Shantanu Pavgi <pavgi(a)uab.edu> >>> > >>> On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote: > >>> > >>> Leandro Hermida wrote: > >>> > >>> Hi Shantanu, > >>> > >>> In your Apache configuration exactly how did you set up an anonymous > >>> > >>> REMOTE_USER just for specific locations like the /datasets/ path? I'm > just > >>> > >>> looking at the Apache docs and the RequestHeader directive has a > context of > >>> > >>> the entire VirtualHost and cannot be put into a Location container so > I'm > >>> > >>> not sure how to do it. > >>> > >>> Hi Leandro, > >>> > >>> See the optional 'env=' argument and docs on the same for ways to make > >>> RequestHeader conditional: > >>> > >>> > http://httpd.apache.org/docs/current/mod/mod_headers.html#requestheader > >>> > >>> So, depending on the path accessed, you should be able to have > >>> mod_rewrite set an environment variable specifying which REMOTE_USER > >>> (real username or fake anonymouse user) should be set. > >>> > >>> You could also just set it as the anonymous user to start with and then > >>> use 'RequestHeader set' to overwrite it with the real username in the > >>> case that a real username is available. > >>> > >>> This is all just from glancing at the docs, though, I have not tried > any > >>> of it out, and this sort of Apache trickery is always difficult to get > >>> right. > >>> > >>> --nate > >>> > >>> > >>> > >>> Leandro, > >>> The RequestHeader has a context of 'directory' as well, which includes > >>> <Directory>, <Location>, <Files>, and <Proxy> containers [1]. So you > should > >>> be able to use it in Location directive. > >>> Following is a configuration snippet related to what Nate described in > his > >>> earlier response. We are setting REMOTE_USER variable to anonymous when > it's > >>> not set/empty. > >>> <Location ~ "/(datasets|history)/"> > >>> AuthType shibboleth > >>> ShibRequireSession off > >>> Require shibboleth > >>> RewriteCond %{LA-U:REMOTE_USER} ="" > >>> RequestHeader set REMOTE_USER "anonymous" > >>> </Location> > >>> Hope this helps. > >>> > >>> 1. > http://httpd.apache.org/docs/current/mod/directive-dict.html#Context > >>> -- > >>> Shantanu. > >>> > > > > > > Leandro, > > > > I realized that above mentioned configuration is wrong. It will set > RequestHeader to 'anonymous' regardless of authentication status. I think > following config should work (still testing). In our case it resides outside > of Location directive now. You may need to adjust it according to your > setup: > > > > {{{ > > # Take the environment variable and set it as a header in the > proxy request. > > RewriteCond %{IS_SUBREQ} ^false$ > > RewriteCond %{LA-U:REMOTE_USER} (.+) > > RewriteRule . - [E=RU:%1] > > # Set RU to anonymous if No REMOTE_USER > > RewriteCond %{IS_SUBREQ} ^false$ > > RewriteCond %{LA-U:REMOTE_USER} ="" > > RewriteRule . - [E=RU:"anonymous"] > > # Set RequestHeader > > RequestHeader set REMOTE_USER %{RU}e > > }}} > > > > > > -- > > Shantanu. > > > > > >