Hi,
I'm trying to debug file uploads using the file browser. I have nginx setup to proxy but not to a sub directory. /usr/sbin/nginx -V nginx version: nginx/1.4.3 --add-module=/usr/local/src/nginx_upload_module-2.2.0
Here are the settings in my universe_wsgi.ini: nginx_upload_store = database/tmp/upload_store nginx_upload_path = /_upload
Here is the nginx config:
user galaxy; worker_processes 1; events { worker_connections 1024; }
http { include /etc/nginx/mime.types; default_type application/octet-stream;
gzip on; gzip_http_version 1.1; gzip_vary on; gzip_comp_level 4; gzip_proxied any; gzip_types text/plain text/css application/x-javascript text/xml applicatio$ gzip_buffers 16 8k; gzip_disable "MSIE [1-6].(?!.*SV1)";
upstream galaxy_app { server localhost:8080; }
log_format main '$remote_addr - $remote_user [$time_local] "$request" ' '$status $body_bytes_sent "$http_referer" ' '"$http_user_agent" "$http_x_forwarded_for"';
access_log /var/log/nginx/access.log main; sendfile on; keepalive_timeout 65; server { listen 80; server_name localhost eugene.imb.nrc.ca; client_max_body_size 10G;
#charset koi8-r; #access_log /var/log/nginx/log/host.access.log main;
location / { proxy_pass http://galaxy_app; proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; }
location /static { alias /software/packages/galaxy/galaxy-dist/static; expires 24h; } location /static/style { alias /software/packages/galaxy/galaxy-dist/static/june_2007_style/blue; expires 24h; } location /static/scripts { alias /software/packages/galaxy/galaxy-dist/static/scripts/packed; } location /favicon.ico { alias /software/packages/galaxy/galaxy_dist/static/favicon.ico; } location /robots.txt { alias /software/packages/galaxy/galaxy-dist/static/robots.txt; }
location /_x_accel_redirect/ { internal; alias /; }
location /_upload { upload_store /software/packages/galaxy/galaxy-dist/database/tmp/upload_store; upload_pass_form_field ""; upload_set_form_field "__${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 /_upload_done { set $dst /tool_runner/index; if ($args ~ nginx_redir=([^&]+)) { set $dst $1; } rewrite "" $dst; }
error_page 500 502 503 504 /50x.html; location = /50x.html { root /usr/share/nginx/html; }
The upload store is on a NFS filesystem. There is nothing in the nginx error log. There is nothing in the paster log. I've noticed that files start to be written to the upload store directory but get cut off by a refresh: -----------------------------234101252030936 Content-Disposition: form-data; name="refresh"
refresh
The upload usually tries again ~10 times, unless manually cutoff earlier, before giving up. The user usually sees that the data is uploading and that message never goes away.
I should mention that I have not yet upgraded to the latest release: $ hg summary parent: 11216:c458a0fe1ba8
I also have debug settings on for galaxy.
Likely some setting I've messed up. I'd be grateful for a point in the right direction. I've looked through the archives and googled bunch without success.
I saw there have been changes to how the upload module works with nginx 1.3.9+. Should I downgrade my nginx if the newer version don't play nicely with galaxy?
Thanks, -Sheldon
Sheldon Briand NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.briand@ssc-spc.gc.ca