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
> }
>
> Cheers
> ___
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