"This link may not be followed from within Galaxy" using nginx and upload module.
Any idea would be appreciated. I get a "This link may not be followed from within Galaxy" after following these steps: Get Data -> Upload File -> File Format: Type "lpe" -> select "lped" from autocomplete list. I've compiled latest stable nginx in CentOS 6.3 with upload module http://www.grid.net.ru/nginx/upload.en.html Galaxy being started by galaxy user nginx started by root user (this scenario reports a nginx worker process owned by galaxy) I'm serving Galaxy at a subdirectory as explained in http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy I'm not using External user authentication I suspect this is a problem in nginx.conf upload module directives. Do you know if it's ok to change location /_x_accel_redirect/ { with location /galaxy/_x_accel_redirect/ { ? Besides I couldn't find an _upload_done directory. Do you have an "_upload_done" or "_upload" directory? Where it's located? This is my nginx.conf server { ... more directives location /galaxy { proxy_pass http://galaxy_app; proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; } location /galaxy/static { alias /home/galaxy/galaxy-dist/static; expires 24h; } ....... # more directives location /galaxy/_x_accel_redirect/ { internal; alias /; } location /galaxy/_upload { upload_store /home/galaxy/galaxy-dist/database/tmp/upload_store; upload_pass_form_field ""; upload_set_form_field "__${upload_field_name}__is_composite" "true"; upload_set_form_field "__${upload_field_name}__keys" "name path"; upload_set_form_field "${upload_field_name}_name" "$upload_file_name"; upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path"; upload_pass_args on; upload_pass /_upload_done; } location /galaxy/_upload_done { set $dst /tool_runner/index; if ($args ~ nginx_redir=([^&]+)) { set $dst $1; } rewrite "" $dst; } } Cheers
On Nov 16, 2012, at 1:15 AM, Marcelo Timmerman wrote:
Any idea would be appreciated. I get a "This link may not be followed from within Galaxy" after following these steps:
Get Data -> Upload File -> File Format: Type "lpe" -> select "lped" from autocomplete list.
I've compiled latest stable nginx in CentOS 6.3 with upload module http://www.grid.net.ru/nginx/upload.en.html Galaxy being started by galaxy user nginx started by root user (this scenario reports a nginx worker process owned by galaxy) I'm serving Galaxy at a subdirectory as explained in http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy I'm not using External user authentication
I suspect this is a problem in nginx.conf upload module directives. Do you know if it's ok to change
location /_x_accel_redirect/ {
with
location /galaxy/_x_accel_redirect/ {
?
Hi Marcelo, For the moment, we can ignore /_x_accel_redirect/, since that is only used for downloading data from Galaxy.
Besides I couldn't find an _upload_done directory. Do you have an "_upload_done" or "_upload" directory? Where it's located?
This is an internal path used by nginx and is not exposed.
This is my nginx.conf
server { ... more directives location /galaxy { proxy_pass http://galaxy_app; proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; } location /galaxy/static { alias /home/galaxy/galaxy-dist/static; expires 24h; } ....... # more directives location /galaxy/_x_accel_redirect/ { internal; alias /; } location /galaxy/_upload { upload_store /home/galaxy/galaxy-dist/database/tmp/upload_store; upload_pass_form_field ""; upload_set_form_field "__${upload_field_name}__is_composite" "true"; upload_set_form_field "__${upload_field_name}__keys" "name path"; upload_set_form_field "${upload_field_name}_name" "$upload_file_name"; upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path"; upload_pass_args on; upload_pass /_upload_done; } location /galaxy/_upload_done { set $dst /tool_runner/index; if ($args ~ nginx_redir=([^&]+)) { set $dst $1; } rewrite "" $dst; }
The problem might be here. Upon upload completion, you redirect to /_upload_done, but the path set up to handle those requests is /galaxy/_upload_done. The other potential problem is that if you haven't set 'nginx_upload_path' in universe_wsgi.ini to '/galaxy/_upload', then the tool form is POSTing to the wrong path. You should be able to use /galaxy/_upload and /galaxy/_upload_done. However, for this to work, you will need to change 'upload_pass' to '/galaxy/_upload_done' above and set 'nginx_upload_path' in universe_wsgi.ini to '/galaxy/_upload'. --nate
}
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participants (2)
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Marcelo Timmerman -
Nate Coraor