12:35 p.m.
Hi all,
I set up the data upload using nginx as described in the wiki
(https://wiki.galaxyproject.org/Admin/Config/nginxProxy, using the subdirectory /galaxy).
The uploaded file also appears inside the uploade_store folder on the galaxy server, but
galaxy does not add the file.
Investigating the log files, I found the corresponding lines in the nginx.error.log:
# Post request is received
2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches
"POST", client: 172.16.17.17, server: , request: "POST /_upload
HTTP/1.1", host: "172.16.12.122", referrer: http://172.16.12.122/galaxy/
# Upload starts
2016/02/29 12:55:37 [info] 13156#0: *4 started uploading file "boxes.txt" to
"/mnt/idrive1/database/tmp/upload_store/0020132707" (field
"files_0|file_data", content type "text/plain"), client: 172.16.17.17,
server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122",
referrer: http://172.16.12.122/galaxy/
# Upload done, the file is present in the given path
2016/02/29 12:55:37 [info] 13156#0: *4 finished uploading file "boxes.txt" to
"/mnt/idrive1/database/tmp/upload_store/0020132707", client: 172.16.17.17,
server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122",
referrer: "http://172.16.12.122/galaxy/"
# Redirection starts?
2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches
"POST", client: 172.16.17.17, server: , request: "POST /_upload
HTTP/1.1", host: "172.16.12.122", referrer:
"http://172.16.12.122/galaxy/"
2016/02/29 12:55:37 [notice] 13156#0: *4 "nginx_redir=([^&]+)" does not
match "", client: 172.16.17.17, server: , request: "POST /_upload
HTTP/1.1", host: "172.16.12.122", referrer:
"http://172.16.12.122/galaxy/"
2016/02/29 12:55:37 [notice] 13156#0: *4 "" matches "/_upload_done",
client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
# Redirection should be done here
2016/02/29 12:55:37 [notice] 13156#0: *4 rewritten data: "/galaxy/api/tools",
args: "", client: 172.16.17.17, server: , request: "POST /_upload
HTTP/1.1", host: "172.16.12.122", referrer:
"http://172.16.12.122/galaxy/"
# ModSecurity seems to block the redirect?
2016/02/29 12:55:37 [info] 13156#0: *4 ModSecurity: invalid "Content-Length"
header, client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches
"GET", client: 172.16.17.17, server: , request: "POST /_upload
HTTP/1.1", host: "172.16.12.122", referrer:
"http://172.16.12.122/galaxy/"
A ModSecurityEnabled off; within the /_upload and /_upload_done of the nginx config did
not help.
Any idea why the Content-Length header causes problems and is blocked by modSec? Any
workaround for ModSec to accept everything that goes from internal to internal?
Thanks for your help!
Best,
Jens
8:29 p.m.
Can you share your nginx config? Perhaps with a gist or something.
-John
On Mon, Feb 29, 2016 at 12:35 PM, Preussner, Jens
<Jens.Preussner(a)mpi-bn.mpg.de> wrote:
Hi all,
I set up the data upload using nginx as described in the wiki
(https://wiki.galaxyproject.org/Admin/Config/nginxProxy, using the
subdirectory /galaxy).
The uploaded file also appears inside the uploade_store folder on the galaxy
server, but galaxy does not add the file.
Investigating the log files, I found the corresponding lines in the
nginx.error.log:
# Post request is received
2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches
"POST",
client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: http://172.16.12.122/galaxy/
# Upload starts
2016/02/29 12:55:37 [info] 13156#0: *4 started uploading file "boxes.txt" to
"/mnt/idrive1/database/tmp/upload_store/0020132707" (field
"files_0|file_data", content type "text/plain"), client:
172.16.17.17,
server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122",
referrer: http://172.16.12.122/galaxy/
# Upload done, the file is present in the given path
2016/02/29 12:55:37 [info] 13156#0: *4 finished uploading file "boxes.txt"
to "/mnt/idrive1/database/tmp/upload_store/0020132707", client:
172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
# Redirection starts?
2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches
"POST",
client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
2016/02/29 12:55:37 [notice] 13156#0: *4 "nginx_redir=([^&]+)" does not
match "", client: 172.16.17.17, server: , request: "POST /_upload
HTTP/1.1",
host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
2016/02/29 12:55:37 [notice] 13156#0: *4 "" matches "/_upload_done",
client:
172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
# Redirection should be done here
2016/02/29 12:55:37 [notice] 13156#0: *4 rewritten data:
"/galaxy/api/tools", args: "", client: 172.16.17.17, server: ,
request:
"POST /_upload HTTP/1.1", host: "172.16.12.122", referrer:
"http://172.16.12.122/galaxy/"
# ModSecurity seems to block the redirect?
2016/02/29 12:55:37 [info] 13156#0: *4 ModSecurity: invalid "Content-Length"
header, client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1",
host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches
"GET",
client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
A ModSecurityEnabled off; within the /_upload and /_upload_done of the nginx
config did not help.
Any idea why the Content-Length header causes problems and is blocked by
modSec? Any workaround for ModSec to accept everything that goes from
internal to internal?
Thanks for your help!
Best,
Jens
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8:34 a.m.
Hi John,
thanks for your answer. The nginx config can be found at
https://gist.github.com/jenzopr/623c3541419ce33f662c
What I did was the following:
1) Stopping both servers, nginx and galaxy
2) Removing all log files and the tmp files in upload_store
3) Restarting the servers
4) Starting a fresh browser session, deleting all cookies.
5) Navigating to my galaxy via the browser (172.16.12.122/galaxy, not
172.16.12.122:8080)
6) Login and upload a file test.txt
The file appears in the upload_store, but this time I got a 403 although I was logged in
properly.
Best,
Jens
-----Original Message-----
From: John Chilton [mailto:jmchilton@gmail.com]
Sent: Mittwoch, 2. März 2016 21:30
To: Preussner, Jens
Cc: galaxy-dev(a)lists.galaxyproject.org
Subject: Re: [galaxy-dev] nginx data upload request never reaches /api/tools
Can you share your nginx config? Perhaps with a gist or something.
-John
On Mon, Feb 29, 2016 at 12:35 PM, Preussner, Jens <Jens.Preussner(a)mpi-bn.mpg.de>
wrote:
Hi all,
I set up the data upload using nginx as described in the wiki
(https://wiki.galaxyproject.org/Admin/Config/nginxProxy, using the
subdirectory /galaxy).
The uploaded file also appears inside the uploade_store folder on the
galaxy server, but galaxy does not add the file.
Investigating the log files, I found the corresponding lines in the
nginx.error.log:
# Post request is received
2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches
"POST",
client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: http://172.16.12.122/galaxy/
# Upload starts
2016/02/29 12:55:37 [info] 13156#0: *4 started uploading file
"boxes.txt" to "/mnt/idrive1/database/tmp/upload_store/0020132707"
(field "files_0|file_data", content type "text/plain"), client:
172.16.17.17,
server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122",
referrer: http://172.16.12.122/galaxy/
# Upload done, the file is present in the given path
2016/02/29 12:55:37 [info] 13156#0: *4 finished uploading file "boxes.txt"
to "/mnt/idrive1/database/tmp/upload_store/0020132707", client:
172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
# Redirection starts?
2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches
"POST",
client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
2016/02/29 12:55:37 [notice] 13156#0: *4 "nginx_redir=([^&]+)" does
not match "", client: 172.16.17.17, server: , request: "POST /_upload
HTTP/1.1",
host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
2016/02/29 12:55:37 [notice] 13156#0: *4 "" matches "/_upload_done",
client:
172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
# Redirection should be done here
2016/02/29 12:55:37 [notice] 13156#0: *4 rewritten data:
"/galaxy/api/tools", args: "", client: 172.16.17.17, server: ,
request:
"POST /_upload HTTP/1.1", host: "172.16.12.122", referrer:
"http://172.16.12.122/galaxy/"
# ModSecurity seems to block the redirect?
2016/02/29 12:55:37 [info] 13156#0: *4 ModSecurity: invalid "Content-Length"
header, client: 172.16.17.17, server: , request: "POST /_upload
HTTP/1.1",
host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches
"GET",
client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
"172.16.12.122", referrer: "http://172.16.12.122/galaxy/"
A ModSecurityEnabled off; within the /_upload and /_upload_done of the
nginx config did not help.
Any idea why the Content-Length header causes problems and is blocked
by modSec? Any workaround for ModSec to accept everything that goes
from internal to internal?
Thanks for your help!
Best,
Jens
___________________________________________________________
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/
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2535
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galaxy-dev@lists.galaxyproject.org
2 comments
2 participants
participants (2)
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John Chilton -
Preussner, Jens