Do you have ``nginx_x_accel_redirect_base = /_x_accel_redirect`` set in
your Galaxy ini file?

Do you know what user nginx runs as?

If yes, do you know if it has access to /home/galaxy/Software/galaxy/
database/files/000/dataset_140.dat?

I'd su to become that nginx user and just make sure it can cd into that
directory and read that file.

If it can't read the directory - my common recommendation is to create a
Galaxy group, make sure the nginx user belongs to it, and ensure all of
Galaxy's data files are group readable.

If the permissions are not the problem - I'm at a bit of a loss.

-John


On Wed, Mar 1, 2017 at 11:35 AM, pieter coussement <
pieter.coussem...@inbiose.com> wrote:

> Hi,
>
> I just updated galaxy, and now I seem to be unable to view the contents of
> the files.
>
> So i'm able to upload, and can work with them and see the attributes.
>
> If however I want to open them ('the eye' on the left), I get an error (as
> do my collegues)
>
> I checked on the full path and the file is there.
>
> permission on the file:
>
> -rw-r--r--  1 galaxy galaxy        16 mrt  1 12:10 dataset_140.dat
>
>
> nginx vhost
>
>         ##
>         # Galaxy
>         ##
>
>         upstream galaxy_app {
>                 server 127.0.0.1:8080;
>         }
>
>         proxy_next_upstream off;
>
>         server {
>                 client_max_body_size 10G;
>                 # ... other server stuff ...
>                 location / {
>                         proxy_pass   http://galaxy_app;
>                         proxy_set_header   X-Forwarded-Host $host;
>                         proxy_set_header   X-Forwarded-For
> $proxy_add_x_forwarded_for;
>                 }
>
>                 location /static {
>                         alias /home/galaxy/Software/galaxy/static;
>                         expires 24h;
>
>                 }
>
>                 location /static/style {
>                         alias /home/galaxy/Software/galaxy/
> static/style/blue;
>                         expires 24h;
>                 }
>
>                 location /static/scripts {
>                         alias /home/galaxy/Software/galaxy/static/scripts;
>                 }
>
>                 location /favicon.ico {
>                         alias /home/galaxy/Software/galaxy/
> static/favicon.ico;
>                 }
>
>                 location /robots.txt {
>                         alias /home/galaxy/Software/galaxy/
> static/robots.txt;
>                 }
>
>                 # serve static content for visualization and interactive
> environment plugins
>                 location ~ ^/plugins/(?<plug_type>.+?)/(?
> <vis_name>.+?)/static/(?<static_file>.*?)$ {
>                         alias /home/galaxy/Software/galaxy/
> config/plugins/$plug_type/$vis_name/static/$static_file;
>                 }
>
>                 location /_x_accel_redirect/ {
>                         internal;
>                         alias /;
>                 }
>
>                 location ~ \.php$ {
>                         fastcgi_pass 127.0.0.1:9000;
>                         include /etc/nginx/conf.d/*.conf;
>                         include /etc/nginx/sites-enabled/*;
>
>                         fastcgi_intercept_errors        on;
>                         error_page 404 /error/404.php;
>                 }
>         }
>
>
> I would guess a permission error of some kind but I seem unable to find
> it.
>
> Nginx spits out:
>
> 2017/03/01 17:23:39 [error] 28783#0: *1457 open()
> "/usr/share/nginx/htmltrue/home/galaxy/Software/galaxy/
> database/files/000/dataset_14
> 0.dat" failed (2: No such file or directory), client: 172.19.40.126,
> server: , request: "GET /datasets/32d48e3506ae8cf7/display/?previ
> ew=True HTTP/1.1", upstream: "http://127.0.0.1:8080/
> datasets/32d48e3506ae8cf7/display/?preview=True"
> <http://127.0.0.1:8080/datasets/32d48e3506ae8cf7/display/?preview=True>,
> host: "172.19.32.42", referrer:
> "http://172.19.32.42/"; <http://172.19.32.42/>
>
> the file is in home/galaxy/Software/galaxy/database/files/000/dataset_
> 140.dat
>
> but the folder /usr/share/nginx/htmltrue does not exists...
>
>
> Any help on this one?
>
> Best regards,
>
> Pieter
> --
>
> *ir. Pieter Coussement, PhD*
> pieter.coussem...@inbiose.com
> +32 (0) 485 42 79 72 <+32%20485%2042%2079%2072>
>
>
>
>
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