Bug? Uploaded files not adding to history (Nginx upload)
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.
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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
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Briand, Sheldon -
Federico Zambelli -
John Chilton