Re: [galaxy-dev] This link may not be followed from within Galaxy using nginx and upload module.
On Nov 16, 2012, at 1:15 AM, Marcelo Timmerman wrote:
Any idea would be appreciated. I get a This link may not be followed from
within Galaxy after following these steps:
Get Data - Upload File - File Format:
Type lpe - select lped from autocomplete list.
I've compiled latest stable nginx in CentOS 6.3 with upload module
http://www.grid.net.ru/nginx/upload.en.html
Galaxy being started by galaxy user
nginx started by root user
(this scenario reports a nginx worker process owned by galaxy)
I'm serving Galaxy at a subdirectory as explained in
http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy
I'm not using External user authentication
I suspect this is a problem in nginx.conf upload module directives.
Do you know if it's ok to change
location /_x_accel_redirect/ {
with
location /galaxy/_x_accel_redirect/ {
?
Hi Marcelo,
For the moment, we can ignore /_x_accel_redirect/, since that is only used for
downloading data from Galaxy.
Besides I couldn't find an _upload_done directory.
Do you have an _upload_done or _upload directory?
Where it's located?
This is an internal path used by nginx and is not exposed.
This is my nginx.conf
server {
... more directives
location /galaxy {
proxy_pass http://galaxy_app;
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
location /galaxy/static {
alias /home/galaxy/galaxy-dist/static;
expires 24h;
}
... # more directives
location /galaxy/_x_accel_redirect/ {
internal;
alias /;
}
location /galaxy/_upload {
upload_store /home/galaxy/galaxy-dist/database/tmp/upload_store;
upload_pass_form_field ;
upload_set_form_field __${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/_upload_done {
set $dst /tool_runner/index;
if ($args ~ nginx_redir=([^]+)) {
set $dst $1;
}
rewrite $dst;
}
The problem might be here. Upon upload completion, you redirect to
/_upload_done, but the path set up to handle those requests is
/galaxy/_upload_done.
The other potential problem is that if you haven't set 'nginx_upload_path' in
universe_wsgi.ini to '/galaxy/_upload', then the tool form is POSTing to the
wrong path.
You should be able to use /galaxy/_upload and /galaxy/_upload_done. However,
for this to work, you will need to change 'upload_pass' to
'/galaxy/_upload_done' above and set 'nginx_upload_path' in universe_wsgi.ini
to '/galaxy/_upload'.
--nate
}
Cheers
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___
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] This link may not be followed from within Galaxy using nginx and upload module.
Any idea would be appreciated. I get a This link may not be followed from
within Galaxy after following these steps:
Get Data - Upload File - File Format:
Type lpe - select lped from autocomplete list.
I've compiled latest stable nginx in CentOS 6.3 with upload module
http://www.grid.net.ru/nginx/upload.en.html
Galaxy being started by galaxy user
nginx started by root user
(this scenario reports a nginx worker process owned by galaxy)
I'm serving Galaxy at a subdirectory as explained in
http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy
I'm not using External user authentication
I suspect this is a problem in nginx.conf upload module directives.
Do you know if it's ok to change
location /_x_accel_redirect/ {
with
location /galaxy/_x_accel_redirect/ {
?
Besides I couldn't find an _upload_done directory.
Do you have an _upload_done or _upload directory?
Where it's located?
This is my nginx.conf
server {
... more directives
location /galaxy {
proxy_pass http://galaxy_app;
proxy_set_header X-Forwarded-Host $host;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
}
location /galaxy/static {
alias /home/galaxy/galaxy-dist/static;
expires 24h;
}
... # more directives
location /galaxy/_x_accel_redirect/ {
internal;
alias /;
}
location /galaxy/_upload {
upload_store /home/galaxy/galaxy-dist/database/tmp/upload_store;
upload_pass_form_field ;
upload_set_form_field __${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/_upload_done {
set $dst /tool_runner/index;
if ($args ~ nginx_redir=([^]+)) {
set $dst $1;
}
rewrite $dst;
}
}
Cheers
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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[galaxy-dev] This link may not be followed from within Galaxy.
Hi, I am getting the error This link may not be followed from within Galaxy. When I try to upload a data file to my local galaxy. I have traced back the error to root.py (RootController class). Could anyone help me with that? Best ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] This link may not be followed from within Galaxy.
On Apr 16, 2012, at 7:13 AM, Eli Reuveni wrote: Hi, I am getting the error “This link may not be followed from within Galaxy.” When I try to upload a data file to my local galaxy. I have traced back the error to root.py (RootController class). Could anyone help me with that? Hi Eli, My initial guess would be that you have enabled the nginx upload settings but that there is a misconfiguration with the upload module. If this is not the case, could you provide the URL that your browser is accessing (you should be able to find it in the Galaxy server log) to receive this error, and some details about whether you are running behind a proxy server, with a prefix, etc.? Thanks, --nate Best ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
