* GeneNetwork Architecture

#+TITLE: Installing GeneNetwork services

* Table of Contents                                                     :TOC:
 - [[#genenetwork-architecture][GeneNetwork Architecture]]
   - [[#introduction][Introduction]]
   - [[#webserver][Webserver]]
   - [[#gnserver-rest][GnServer (REST)]]

** Introduction

This document describes the architecture of GN2. Because GN2 is
evolving, only a high-level overview is given here.

** Webserver

The main [[https://github.com/genenetwork/genenetwork2][GN2 webserver]] is built on [[http://flask.pocoo.org/][Python flask]] and this GN2 source
code can be found on [[https://github.com/genenetwork/genenetwork2/tree/master/wqflask/wqflask][github]] in the wqflask directory. The routing
tables are defined in [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/views.py][views.py]]. For example the main page is loaded
from a template named [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/index_page.htm][index_page.html]] in the [[https://github.com/genenetwork/genenetwork2/tree/master/wqflask/wqflask/templates][templates]] directory. In
the template you can find get the form gets filled by a Javascript
routine defined in [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/static/new/javascript/dataset_select_menu.js][data_select_menu.js]] which picks up a static JSON
file for the menu. This static file is generated with
[[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/maintenance/gen_select_dataset.py][gen_select_dataset.py]].  Note that this JSON data is served by
gn_server in the latest version, see [[#gnserver-rest][GnServer (REST)]].

When you hit a search with, for example,
'http://localhost:5003/search?species=mouse&group=BXD&type=Hippocampus+mRNA&dataset=HC_M2_0606_P&search_terms_or=&search_terms_and=MEAN%3D%2815+16%29+LRS%3D%2823+46%29+&FormID=searchResult'
it has the menu items as parameters. According to the routing table,
the search is executed and Redis caching is used (we'll probably
change that to the level of the gn_server). The logic is in
search_result.py which invokes database functions in
wqflask/dbFunction/webqtlDatabaseFunction.py, for example. The
receiving template lives at [[https://github.com/genenetwork/genenetwork2/blob/master/wqflask/wqflask/templates/search_result_page.html][search_result_page.html]].

** GnServer (REST)

The [[https://github.com/genenetwork/gn_server][GnServer REST API]] is built on high performance [[http://elixir-lang.org/][Elixir]] with [[https://github.com/falood/maru][Maru]].
Mainly the GnServer serves JSON requests, for example to fetch data
from the database. To get the menu data in YAML you can do something like

: curl localhost:8880/int/menu/main.json|ruby extra/json2yaml.rb

(json2yaml.rb is in the gn_server repo).