1 files changed, 38 insertions, 6 deletions
diff --git a/doc/Architecture.org b/doc/Architecture.org
index c263d3b9..b9e8e355 100644
--- a/doc/Architecture.org
+++ b/doc/Architecture.org
@@ -1,5 +1,13 @@
 * 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
@@ -7,9 +15,33 @@ evolving, only a high-level overview is given here.
 
 ** Webserver
 
-The 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]].
+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]].
+
+For what happens at the database level see [[database.org]].
+
+** 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).