Bug? Uploaded files not adding to history (Nginx upload)

classic Classic list List threaded Threaded
5 messages Options
| Threaded
Open this post in threaded view
|

Bug? Uploaded files not adding to history (Nginx upload)

Federico Zambelli-2
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/
| Threaded
Open this post in threaded view
|

Re: Bug? Uploaded files not adding to history (Nginx upload)

John Chilton-4
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
<[hidden email]> 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/
| Threaded
Open this post in threaded view
|

Re: Bug? Uploaded files not adding to history (Nginx upload)

Federico Zambelli-2
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
> <[hidden email]> 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/
| Threaded
Open this post in threaded view
|

Re: Bug? Uploaded files not adding to history (Nginx upload)

Briand, Sheldon
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 [[hidden email]] On Behalf Of Federico Zambelli [[hidden email]]
Sent: Friday, February 06, 2015 8:18 AM
To: John Chilton
Cc: [hidden email]
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
> <[hidden email]> 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/
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Bug? Uploaded files not adding to history (Nginx upload)

Federico Zambelli-2
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 $dst /galaxy/api/tools;
>
> https://wiki.galaxyproject.org/Admin/Config/nginxProxy
>
> -Sheldon
>
>
> ________________________________________
> From: galaxy-dev [[hidden email]] On Behalf Of Federico Zambelli [[hidden email]]
> Sent: Friday, February 06, 2015 8:18 AM
> To: John Chilton
> Cc: [hidden email]
> Subject: Re: [galaxy-dev] Bug? Uploaded files not adding to history (Nginx upload)
>
> Actually we had a quite old version of nginx running, now I have updated
> it to the latest stable 1.6.2 (plus nginx-upload-module-2.2) but the
> issue is still here. The file is correctly uploaded, I can see it in the
> tmp upload directory configured in galaxy.ini but then it is not loaded
> in the history. If I disable nginx upload then all works fine.
>
> my nginx upload entries in galaxy.ini are:
>
> nginx_upload_store = /home/galaxy/galaxy-dist/database/tmp/upload_store
> nginx_upload_path = _upload
>
> In the nginx conf file, for Galaxy uploads I have:
>
>    location /galaxy/_upload {
>               upload_store
> /home/galaxy/galaxy-dist/database/tmp/upload_store;
>               upload_pass_form_field "";
>               upload_set_form_field
> "__${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
>> <[hidden email]> 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/
>

___________________________________________________________
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/