AmiGO is the public interface for the Gene Ontology.
JavaScript Perl CSS Emacs Lisp Python Gherkin
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bin
conf
deployment/ansible
external
golr
java/lib
javascript
metadata
perl
scripts
staging
static
templates/html/bs3
test-app
.gitignore
INSTALL.org
LICENSE
Makefile
README.md
gulpfile.js
install
package.json
version-patch.lvl

README.md

Overview

This README file will be filled out more in the future. However, for the time being, please see the AmiGO 2 Manual for more details about the code and installation. You may also be interested in the related information found in BBOP JS.

Installation

The main installation information is available on the wiki.

Jenkins (example)

Loading

This is a load example using this configuration.

## Get to the app home and make sure we're in the right place.
cd /home/bbop/local/src/git/amigo
git reset --hard && git pull

## Get the environment and variables ready.
npm install
cp conf/examples/amigo.yaml.tomodachi conf/amigo.yaml
## Need to generate config.pl
./node_modules/.bin/gulp install

## Do the load.
./node_modules/.bin/gulp message-load-start
/bin/rm -f /tmp/golr_timestamp.log
./node_modules/.bin/gulp golr-purge
./node_modules/.bin/gulp check-ontology-data
./node_modules/.bin/gulp load-all
./node_modules/.bin/gulp message-load-clear

Deployment & Unit Tests

This is an example automatic deployment and unit/app testing using this configuration.

## I believe Xvfb should die on shell exit?
Xvfb :1 -screen 5 1024x768x8 &

## Get to the app home and make sure we're in the right place.
cd /home/bbop/local/src/git/amigo
git pull && git reset --hard

## Get the environment and variables ready.
npm install
cp conf/examples/amigo.yaml.tomodachi conf/amigo.yaml
## Need to generate config.pl
./node_modules/.bin/gulp install

## Make the proper python virtualenv setup with the libs we need.
cd test-app/behave
virtualenv `pwd`
source bin/activate
pip install selenium behave jsonpath-rw
## Get back to top.
cd ../..

## Run unit tests against AmiGO labs (master).
DISPLAY=:1.5 ./node_modules/.bin/gulp tests

## Pop out of our wonderland.
deactivate