sckan-composer

Prerequisites

Python

The deployment process is based on Python 3.9+ scripts. It is recommended to setup a virtual environment first.

With venv:

python3 -m venv venv
source venv/bin/activate

With pyenv (get it here):

pyenv virtualenv 3.9.15 composer
pyenv activate composer

With (mini)conda (get it here):

conda create --name composer python=3.9
conda activate composer

Optional: install docker and docker-compose (get it here)

docker and docker-compose is needed to build and run the composer and database images on a Docker virtual environment. This step is an optional step

Development setup

Running locally

cd backend
# make sure your virtual env is activated
# and install the requirements
pip3 install --upgrade -r requirements.txt
# run the migrations
python3 manage.py migrate
# run the development server (https)
python3 manage.py runsslserver

Running the Backend on docker with docker-compose

the command below will start a docker container that maps/uses the backend folder into the container. It will also start the Django development server with DEBUG=True

BUILDKIT_PROGRESS=plain docker-compose -f docker-compose-dev.yaml up --build

Running the PostgreSQL database with docker-compose

the command below will start a docker container that runs the PostgreSQL database. To use it within your development Django server you need to set the following env vars in your launch(file)

USE_PG=True
DB_HOST=localhost
DB_PORT=5432
DB_NAME=composer
DB_USER=composer
DB_PASSWORD=composer

To start the database server run this command:

docker-compose --file docker-compose-db.yaml up --build

to stop the database run this command:

docker-compose -f docker-compose-db.yaml down

Example to run the backend using the Docker PostgreSQL database

cd backend

export USE_PG=True
export DB_HOST=localhost
export DB_PORT=5432
export DB_NAME=composer
export DB_USER=composer
export DB_PASSWORD=composer

python ./manage.py runsslserver

Ingest sample NLP data

The git repository comes with some sample NLP data. This data can be ingested using the "ingest_nlp_sentence" management command

cd backend
python3 manage.py ingest_nlp_sentence ./composer/resources/pmc_oai_202209.csv

Ingest sample Anatomical Entities data

The git repository comes with some sampleAnatomical Entities data. This data can be ingested using the "ingest_anatomical_entities" management command

cd backend
python3 manage.py ingest_anatomical_entities ./composer/resources/anatomical_entities.csv

Open the admin page

there will be a superuser created with username/password: admin/admin

browse the Django admin interface

Install openapi generator

For generating the frontend api client use the openapi generator install:

npm install -g @openapitools/openapi-generator-cli

and then run

cd frontend
./genapi.sh

ORCID login setup

browse to ORCID dev tools and create a new api configure settings.py with the new key and secret

Production setup

Running on docker with docker-compose the command below will start two docker containers: backend server and database server the backend server has a persistent disk connected for it's media files the database server has a persistent disk connected for the data

docker-compose up --build

to stop:

docker-compose down

Open the admin page

there will be a superuser created with username/password: admin/admin

browse the Django admin interface