[galaxy-dev] View uploaded files

1 Mar 2017

      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", 
host: "172.19.32.42", referrer:
"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.coussement@inbiose.com <mailto:pieter.coussement@inbiose.com>
+32 (0) 485 42 79 72

www.inbiose.com <http://www.inbiose.com>
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[galaxy-dev] View uploaded files

pieter coussement