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Diffstat (limited to 'doc')
| -rw-r--r-- | doc/Architecture.org | 44 | ||||
| -rw-r--r-- | doc/README.org | 1 |
2 files changed, 38 insertions, 7 deletions
diff --git a/doc/Architecture.org b/doc/Architecture.org index c263d3b9..e8ffe69b 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 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). + + diff --git a/doc/README.org b/doc/README.org index 3754dbbd..b3c78f29 100644 --- a/doc/README.org +++ b/doc/README.org @@ -1,4 +1,3 @@ - #+TITLE: Installing GeneNetwork services * Table of Contents :TOC: |