Franken Plot API

Setup and Prerequisite installation

Back-End

cd franken_api

    python setup.py  install
    pip install -r requirements.txt
    pip install .

Run application

    franken_api -p 5000

Run DB Migration script:

sudo docker exec -it probio_ui_docker_postgress_1 bash
su postgres
psql
CREATE USER referral_writer WITH ENCRYPTED PASSWORD '<password: this should match with password in flask app settings.py>';
CREATE DATABASE referrals;
CREATE DATABASE curation;
GRANT ALL PRIVILEGES ON DATABASE referrals TO referral_writer;
GRANT ALL PRIVILEGES ON DATABASE curation TO referral_writer;
exit

python franken_api/migrate.py db init --multidb
python franken_api/migrate.py db migrate
python franken_api/migrate.py db upgrade

Generate Profile Summary for Project

    cd franken_api/genomic_profile_lookup/
    python read_curation_info_store_postgresql_final.py '<nfs-autoseq-path>' '<project-name>

ENV Setup in the .bashrc

    export DATABASE_URL="postgresql+psycopg2://<POSTGRES_USER>:<POSTGRES_PWD>@127.0.0.1:5432/<REFERRAL_DB>"
    export CURATION_DB_URL="postgresql+psycopg2://<POSTGRES_USER>:<POSTGRES_PWD>@127.0.0.1:5432/<CURATION_DB>"
    export LEADERBOARD_DB_URL="postgresql+psycopg2://<POSTGRES_USER>:<POSTGRES_PWD>@127.0.0.1:5432/<LEADERBOARD_DB>"
    export IPCM_DB_URL="postgresql+psycopg2://<POSTGRES_USER>:<POSTGRES_PWD>@127.0.0.1:5432/<IPCM_DB>"