Uploads via Nginx proxy fail after upgrade to current release

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Uploads via Nginx proxy fail after upgrade to current release

Hans-Georg Sommer
Hi,

after updating Galaxy to 18.05 (from 17.05) the file upload doesn't work
anymore, but shows an Internal Server Error (500) in the status column
of the upload form.

We use a nginx proxy also for uploads, configured as described in [1],
galaxy.ini contains the line 'nginx_upload_path = /_upload'.

The nginx access logs show, that the upload requests seem to go to the
wrong location ('/api/uploads' instead of '/_upload'):
0.0.0.0 - - [06/Jun/2018:10:44:43 +0200] "POST /api/uploads HTTP/1.1"
500 193 "https://galaxy.gwdg.de/"

I searched the release notes and the github issues, but wasn't able to
find anything besides [2], which sounds similar but does not give much
information.

Thanks for your help,

Hans-Georg

[1] https://docs.galaxyproject.org/en/latest/admin/nginx.html
[2] https://biostar.usegalaxy.org/p/25870/

--
------------------------------------------------------------------------
Hans-Georg Sommer
Arbeitsgruppe "Anwendungs- und Informationssysteme"
E-Mail: [hidden email]
------------------------------------------------------------------------
Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen
(GWDG)
Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de
Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: [hidden email]
Service-Hotline: Tel.: +49 551 201-1523, E-Mail: [hidden email]

Geschäftsführer: Prof. Dr. Ramin Yahyapour
Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau
Sitz der Gesellschaft: Göttingen
Registergericht: Göttingen, Handelsregister-Nr. B 598
------------------------------------------------------------------------
Zertifiziert nach ISO 9001
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Re: Uploads via Nginx proxy fail after upgrade to current release

Ignacio EGUINOA
Hi,

I'm also experiencing what I think is the same problem after upgrading to v18.05 (from 17.09). Some more info on this:
In my case I've tried this with and without the proxy (Apache) and using either uWSGI or Paste as http servers and this changes nothing.
I have 2 servers and in one of them the upload works perfectly fine after the upgrade to v18.05. here are barely any differences in the framework code (just a few custom changes for the private instance) and it also works with Apache as proxy so I really don't understand where is the error coming from.
If i try to upload a file to a data library from a path in the server then it works ok.
I get the same error as Hans-Georg Somme in the upload ->    Warning: Internal Server Error (500)
The error I get in the logs is:

galaxy.web.framework.decorators ERROR 2018-06-06 15:17:40,976 [p:17537,w:1,m:0] [uWSGIWorker1Core3] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 154, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/galaxy/api/uploads.py", line 43, in create
    chunk_size = os.fstat(session_chunk.file.fileno()).st_size
AttributeError: 'cStringIO.StringO' object has no attribute 'fileno'


Hope this clarifies a bit.
Ignacio



From: "Hans-Georg Sommer" <[hidden email]>
To: "galaxy-dev" <[hidden email]>
Sent: Wednesday, June 6, 2018 11:13:40 AM
Subject: [galaxy-dev] Uploads via Nginx proxy fail after upgrade to current        release
Hi,

after updating Galaxy to 18.05 (from 17.05) the file upload doesn't work
anymore, but shows an Internal Server Error (500) in the status column
of the upload form.

We use a nginx proxy also for uploads, configured as described in [1],
galaxy.ini contains the line 'nginx_upload_path = /_upload'.

The nginx access logs show, that the upload requests seem to go to the
wrong location ('/api/uploads' instead of '/_upload'):
0.0.0.0 - - [06/Jun/2018:10:44:43 +0200] "POST /api/uploads HTTP/1.1"
500 193 "https://galaxy.gwdg.de/"

I searched the release notes and the github issues, but wasn't able to
find anything besides [2], which sounds similar but does not give much
information.

Thanks for your help,

Hans-Georg

[1] https://docs.galaxyproject.org/en/latest/admin/nginx.html
[2] https://biostar.usegalaxy.org/p/25870/

--
------------------------------------------------------------------------
Hans-Georg Sommer
Arbeitsgruppe "Anwendungs- und Informationssysteme"
E-Mail: [hidden email]
------------------------------------------------------------------------
Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen
(GWDG)
Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de
Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: [hidden email]
Service-Hotline: Tel.: +49 551 201-1523, E-Mail: [hidden email]

Geschäftsführer: Prof. Dr. Ramin Yahyapour
Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau
Sitz der Gesellschaft: Göttingen
Registergericht: Göttingen, Handelsregister-Nr. B 598
------------------------------------------------------------------------
Zertifiziert nach ISO 9001
------------------------------------------------------------------------
___________________________________________________________
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/

___________________________________________________________
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:
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Re: Uploads via Nginx proxy fail after upgrade to current release

Ignacio EGUINOA
Hi again,

I'm still not sure if this is the same error as Hans-Georg Sommer but in my case I've just noticed that the error only occurs with files SMALLER than ~1KB




From: "Ignacio Eguinoa" <[hidden email]>
To: "Hans-Georg Sommer" <[hidden email]>
Cc: "galaxy-dev" <[hidden email]>
Sent: Wednesday, June 6, 2018 3:43:47 PM
Subject: Re: [galaxy-dev] Uploads via Nginx proxy fail after upgrade to current        release
Hi,

I'm also experiencing what I think is the same problem after upgrading to v18.05 (from 17.09). Some more info on this:
In my case I've tried this with and without the proxy (Apache) and using either uWSGI or Paste as http servers and this changes nothing.
I have 2 servers and in one of them the upload works perfectly fine after the upgrade to v18.05. here are barely any differences in the framework code (just a few custom changes for the private instance) and it also works with Apache as proxy so I really don't understand where is the error coming from.
If i try to upload a file to a data library from a path in the server then it works ok.
I get the same error as Hans-Georg Somme in the upload ->    Warning: Internal Server Error (500)
The error I get in the logs is:

galaxy.web.framework.decorators ERROR 2018-06-06 15:17:40,976 [p:17537,w:1,m:0] [uWSGIWorker1Core3] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 154, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/galaxy/api/uploads.py", line 43, in create
    chunk_size = os.fstat(session_chunk.file.fileno()).st_size
AttributeError: 'cStringIO.StringO' object has no attribute 'fileno'


Hope this clarifies a bit.
Ignacio



From: "Hans-Georg Sommer" <[hidden email]>
To: "galaxy-dev" <[hidden email]>
Sent: Wednesday, June 6, 2018 11:13:40 AM
Subject: [galaxy-dev] Uploads via Nginx proxy fail after upgrade to current        release
Hi,

after updating Galaxy to 18.05 (from 17.05) the file upload doesn't work
anymore, but shows an Internal Server Error (500) in the status column
of the upload form.

We use a nginx proxy also for uploads, configured as described in [1],
galaxy.ini contains the line 'nginx_upload_path = /_upload'.

The nginx access logs show, that the upload requests seem to go to the
wrong location ('/api/uploads' instead of '/_upload'):
0.0.0.0 - - [06/Jun/2018:10:44:43 +0200] "POST /api/uploads HTTP/1.1"
500 193 "https://galaxy.gwdg.de/"

I searched the release notes and the github issues, but wasn't able to
find anything besides [2], which sounds similar but does not give much
information.

Thanks for your help,

Hans-Georg

[1] https://docs.galaxyproject.org/en/latest/admin/nginx.html
[2] https://biostar.usegalaxy.org/p/25870/

--
------------------------------------------------------------------------
Hans-Georg Sommer
Arbeitsgruppe "Anwendungs- und Informationssysteme"
E-Mail: [hidden email]
------------------------------------------------------------------------
Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen
(GWDG)
Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de
Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: [hidden email]
Service-Hotline: Tel.: +49 551 201-1523, E-Mail: [hidden email]

Geschäftsführer: Prof. Dr. Ramin Yahyapour
Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau
Sitz der Gesellschaft: Göttingen
Registergericht: Göttingen, Handelsregister-Nr. B 598
------------------------------------------------------------------------
Zertifiziert nach ISO 9001
------------------------------------------------------------------------
___________________________________________________________
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/

___________________________________________________________
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/

___________________________________________________________
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/