Dear all,
I'm attempting to integrate the genome viewer AnnoJ into my application. To
allow visitors to view data provided by another service, I need to
configure a reverse proxy. This is easy enough to do in Apache, but I've
been having problems doing this in web2py. I've tried several variations
using the routes.py file:
routes_in = (
(r'matapax/default/annoj/(http://neomorph\.salk\.edu/epigenome/fetchers/arabidopsis_thaliana\.php)',
r'\1'),
(r'matapax/default/annoj/(http://neomorph\.salk\.edu/epigenome/fetchers/models/tair9\.php)',
r'\1')
)
1. With/without raw string (r'')
2. With/without 'matapax/default' in front of the strings (my application
is called matapax, controller is default and function is annoj)
The url I'm trying to proxy for is:
"http:/neomorph.salk.edu/epigenome/fetchers/arabidopsis_thaliana.php"
Example variables: "?_dc=1331908909967&action=syndicate" (this should work
if typed directly into the web browser url).
Hopefully that was a little clearer than mud. Does anybody have any clues
how to get an AnnoJ instance up and running with gene models from the salk
url?
Yours Sincerely,
Liam
The function itself returns an empty dictionary at the moment. The view
looks like the example "Creating an AnnoJ instance" shown below.
Creating an AnnoJ instance: http://www.annoj.org/instances/create.shtml
Configuring an AnnoJ instance:
http://www.annoj.org/instances/configure.shtml
AnnoJ reverse proxy for Apache: http://www.annoj.org/instances/proxy.shtml
My AnnoJ configuration file:
//The Anno-J configuration object
AnnoJ.config = {
//List of configurations for all tracks in the Anno-J instance
tracks : [
{
id : 'models',
name : 'Gene Models',
type : 'ModelsTrack',
path : 'Annotation models',
data :
'matapax/default/annoj/http://neomorph.salk.edu/epigenome/fetchers/models/tair9.php',
height : 80,
showControls : true
}
],
//A list of tracks that will be active by default (use the ID of
the track)
active : [
'models'
],
//Address of service that provides information about this genome
genome : 'matapax/default/annoj
/http://neomorph.salk.edu/epigenome/fetchers/arabidopsis_thaliana.php',
//Address of service that stores / loads user bookmarks
bookmarks : 'matapax/default/annoj
/http://neomorph.salk.edu/epigenome/fetchers/arabidopsis_thaliana.php',
//A list of stylesheets that a user can select between (optional)
stylesheets : [],
//The default 'view'. In this example, chr1, position 1, zoom ratio
20:1.
location : {
assembly : '1',
position : 1,
bases : 20,
pixels : 1
},
//Site administrator contact details (optional)
admin : {
name : 'Liam Childs',
email : '[email protected]',
notes : 'Golm, Germany'
}
};
