The AraGWAS backend is a django app that serves as a REST endpoint for the AraGWAS frontend.
pip install -r requirements.txt
Before the AraGWAS backend can be used, the RabbitMQ server must be started and the genotypes need to be indexed in the elasticserach database
To make it easy to get started, the docker-compose.yml file will start both services.
docker-compose up -d elasticsearch1 amqp1
To get the genotype information indexed in the ES database, run the init_elasticsearch.sh script. This has to be done only once.
./init_elasticserach.sh
This will download the data and start the indexing proceess, which can take a while (~ 15 minutes). Afterwards you can start the backend with the command below.
./manage runserver
In the case of changes in the elasticsearch template, reindexing must be performed. The procedure includes loading all necessary libraries from the project folder and erase the index using.
es.indices.delete(index='aragwas')
Where the name of the index can also be geno_chrX for the genotypes index.
Once this is done, the new index can be created by loading the json template and creating the new index:
aragwas_settings = json.load(open(path_to_template, 'r'))
es.indices.put_template('aragwas', aragwas_settings)
Then, the index can be populated by the individual comments
./manage.py index_study --permutations path_to_permutations_file