Re: [galaxy-dev] Bug? Uploaded files not adding to history (Nginx upload)

6 Feb 2015


      Thank you very much Sheldon, that fixed it!
My bad I did not check the documentation to see if something had changed.

Cheers,
Federico

Il 06/02/15 13:48, Briand, Sheldon ha scritto:
...
Hi,
There was a change made recently.  I ran into it as well.  Look at this section of the nginx conf:
location /_upload_done {
              set $dst /galaxy/tool_runner/index;
              if ($args ~ nginx_redir=([^&]+)) {
                  set $dst $1;
              }
Change the set $dst line to:
set $dst /galaxy/api/tools;
https://wiki.galaxyproject.org/Admin/Config/nginxProxy
-Sheldon
________________________________________
From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of Federico Zambelli [federico.zambelli@gmail.com]
Sent: Friday, February 06, 2015 8:18 AM
To: John Chilton
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Bug? Uploaded files not adding to history (Nginx upload)
Actually we had a quite old version of nginx running, now I have updated
it to the latest stable 1.6.2 (plus nginx-upload-module-2.2) but the
issue is still here. The file is correctly uploaded, I can see it in the
tmp upload directory configured in galaxy.ini but then it is not loaded
in the history. If I disable nginx upload then all works fine.
my nginx upload entries in galaxy.ini are:
nginx_upload_store = /home/galaxy/galaxy-dist/database/tmp/upload_store
nginx_upload_path = _upload
In the nginx conf file, for Galaxy uploads I have:
location /galaxy/_upload {
              upload_store
/home/galaxy/galaxy-dist/database/tmp/upload_store;
              upload_pass_form_field "";
              upload_set_form_field
"__${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"
"$upload_tmp_path";
              upload_pass_args on;
              upload_pass /_upload_done;
          }
location /galaxy/library_common/_upload {
              upload_store
/home/galaxy/galaxy-dist/database/tmp/upload_store;
              upload_pass_form_field "";
              upload_set_form_field
"__${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 /_upload_done {
              set $dst /galaxy/tool_runner/index;
              if ($args ~ nginx_redir=([^&]+)) {
                  set $dst $1;
              }
and it worked fine 'til I updated to the newest Galaxy rel.
I need to fix this issue before upgrading the production server.
Thanks,
F.
Il 06/02/15 04:19, John Chilton ha scritto:
...
I believe we updated usegalaxy.org and Bjoern Docker galaxy images to
the latest Galaxy release - both which leverage this feature and
didn't encounter issues with either. Is it possible you updated nginx
as part of the release as well? At least in the past the upload
feature has had problems with compatibility across various versions of
nginx.
-John
On Tue, Feb 3, 2015 at 7:53 AM, Federico Zambelli
<federico.zambelli@gmail.com> wrote:
...
Hi everybody,
I have recently updated our lab Galaxy instance to the latest stable
latest_2015.01.13. I have now a problem with uploaded files: they are not
added to history.
The problem disappears if I disable the nginx upload feature (that worked
just fine until the update). Maybe it is of help to know that the files are
correctly uploaded to the "nginx_upload_store" directory configured in
galaxy.ini but then they are not added to the current history.
Best,
Federico Z.
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