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Diffstat (limited to 'doc')
| -rw-r--r-- | doc/Architecture.org | 60 | ||||
| -rw-r--r-- | doc/database.org | 1 |
2 files changed, 50 insertions, 11 deletions
diff --git a/doc/Architecture.org b/doc/Architecture.org index ed19889c..9a561568 100644 --- a/doc/Architecture.org +++ b/doc/Architecture.org @@ -1,19 +1,19 @@ -* GeneNetwork Architecture - #+TITLE: Installing GeneNetwork services * Table of Contents :TOC: - - [[#genenetwork-architecture][GeneNetwork Architecture]] - - [[#introduction][Introduction]] - - [[#webserver][Webserver]] - - [[#gnserver-rest][GnServer (REST)]] + - [[#introduction][Introduction]] + - [[#webserver][Webserver]] + - [[#gnserver-rest][GnServer (REST)]] + - [[#database-][Database ]] + - [[#phenotypes][Phenotypes]] + - [[#genotypes][Genotypes]] -** Introduction +* Introduction This document describes the architecture of GN2. Because GN2 is evolving, only a high-level overview is given here. -** Webserver +* 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 @@ -44,7 +44,7 @@ Consortium M430v2 (Jun06) PDNN to find all records with MEAN between 15 and 16 and with LRS between 23 and 46.'. Then the results are added to a table which is displayed using a JS [[https://datatables.net/][DataTable container]]. -** GnServer (REST) +* 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 @@ -52,4 +52,44 @@ 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). +(json2yaml.rb is in the gn_server repo). For the current API definition +see [[https://github.com/genenetwork/gn_server/doc/API.md][GnServer REST API]] documentation. + +* Database + +** Phenotypes + +Phenotypes are stored in the SQL database. For what happens at the +database level see [[database.org]]. A test database can be downloaded - +see the installation [[./README.org][instructions]]. + +** Genotypes + +Genotypes are stored in genotype files. These are part of the GNU Guix +distribution, see the installation [[./README.org][instructions]]. Genotype files are +currently in GN1 format, and will be aligned with the R/qtl2 format. Now it is +for BXD.geno: + +#+begin_src js +@name:BXD +@type:riset +@mat:B +@pat:D +@het:H +@unk:U +Chr Locus cM Mb BXD1 BXD2 BXD5 BXD6 BXD8 BXD9 BXD11 BXD12 BXD13 BXD14 BX +D15 BXD16 BXD18 BXD19 BXD20 BXD21 BXD22 BXD23 BXD24a BXD24 BXD25 BXD27 BXD28 BX +D29 BXD30 BXD31 BXD32 BXD33 BXD34 BXD35 BXD36 BXD37 BXD38 BXD39 BXD40 BXD41 BXD4 +2 BXD43 BXD44 BXD45 BXD48 BXD49 BXD50 BXD51 BXD52 BXD53 BXD54 BXD55 BXD56 BXD59 +BXD60 BXD61 BXD62 BXD63 BXD64 BXD65 BXD66 BXD67 BXD68 BXD69 BXD70 BXD71 BXD72 BX +D73 BXD74 BXD75 BXD76 BXD77 BXD78 BXD79 BXD80 BXD81 BXD83 BXD84 BXD85 BXD86 BXD8 +7 BXD88 BXD89 BXD90 BXD91 BXD92 BXD93 BXD94 BXD95 BXD96 BXD97 BXD98 BXD99 BXD100 + BXD101 BXD102 BXD103 +1 rs6269442 0.0 3.482275 B B D D D B B D B B D D B D D D D B B B D B D D B B B +B B B B B B D B D B B D B B H H B D B B H H B B D D D D D B B H B B B B D B D B +D D D D D H B D D B D B B D D B D D B B B B B B B D +1 rs6365999 0.0 4.811062 B B D D D B B D B B D D B D D D D B B B D B D D B B B +B B B B B B D B D B B D B B H H B D B B H H B B D D D D D B B H B B B B D B D B +D D D D D H B D D B D B B D D B D D B B B B B B U D +etc +#+end_src diff --git a/doc/database.org b/doc/database.org index df34e7ed..2c7dc887 100644 --- a/doc/database.org +++ b/doc/database.org @@ -506,7 +506,6 @@ select count(*) from ProbeSet limit 5; +------+--------+----------+----------+--------+----------------------------------------------+------+-----------+----------+--------+-----------+------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+-----------+--------------+-------------+--------+----------+-------------------------+-----------------------+----------------------+-------------------------+-----------------------+------------------+----------------------+------+----------+---------------+--------------+------+---------+----------+---------+----------+--------------------------+---------------------+---------+-----------+-----------------------------+---------------------------+--------------+-------------+-----------+-------------+------------+---------+------------+----------+-----------+------------+------------+---------------+---------+-----------+---------+------------------+-------------+------+--------+-------------+----------------+-----------------+ 2 rows in set (0.00 sec) - ** ProbeSetXRef (phenotypes/dataset_name.json) For every probe set (read dataset measuring point): |