metabolitics-api-v3

This is the updated version of Metabolitics API.

Developing on Linux

1. Clone metabolitics-api-v3 repository. Checkout to your branch.

   https://github.com/itu-bioinformatics-database-lab/metabolitics-api-v3.git

2. Install Anaconda. Create a Conda environment.

   conda config --append channels conda-forge

   conda create --name menv python=3.5.2

   conda activate menv

3. Install required Python packages.

   pip install -r requirements.txt

4. Create a local PostgreSQL database. Set up connection in src/app/config.py file.

5. Create database schema under src directory.

   python main.py migrate

6. Install Redis.

7. Generate secret.txt file under src directory.

   python main.py generate-secret

8. Start the API under src directory.

   python main.py run-api

9. Start Celery worker under src directory.

   python main.py run-celery

10. Start Celery beat under src directory.

    python main.py run-celery-beat

Developing Inside a Docker Container

Developing Metabolitics API inside a Docker container built from Dockerfile ensures a fully compatible development environment with all of the features of Visual Studio Code.

1. Install and configure Docker for your operating system.

2. Install Visual Studio Code.

3. Install the Dev Containers extension from Visual Studio Code Extensions.

4. Clone metabolitics-api-v3 Git repository by running the below command in a terminal.

   git clone https://github.com/itu-bioinformatics-database-lab/metabolitics-api-v3.git

5. Open Visual Studio Code and run Dev Containers: Open Folder in Container... command from View -> Command Palette.

6. Select metabolitics-api-v3 repository.

7. Select From 'Dockerfile' from Add Dev Container Configuration Files dialog.

8. Don't select any features and click Ok.

9. Wait for the container to install.

10. To generate secret.txt file, run the below command in a terminal under src directory.

    python main.py generate-secret

11. To resolve Git line ending issues in the container (resulting in many modified files), see below link:

    https://code.visualstudio.com/docs/devcontainers/tips-and-tricks

12. To create a local PostgreSQL database in Docker, run the below command in a terminal.

    docker run --name postgres -p 5432:5432 -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=boss123 -e POSTGRES_DB=postgres -d postgres:9.4

13. To see the IP address of the database, run the below command in a terminal.

    docker inspect postgres

14. Set connection details of the database using the IP address from the step 13 in src/app/config.py.

    SQLALCHEMY_DATABASE_URI = 'postgresql://postgres:[email protected]/postgres'

15. To migrate data to the newly created database, run the below command in a terminal under src directory.

    python main.py migrate

16. To install Redis server in Docker, run the below command in a terminal.

    docker run --name redis -p 6379:6379 -d redis

17. To connect Metabolitics Api and Redis, run below commands in a terminal one by one.

    docker network create metabolitics

    docker network connect metabolitics <metabolitics-api>

    docker network connect metabolitics redis

18. To run metabolitics-api-v3, run the below command under src directory and open localhost:5000.

    gunicorn --bind 0.0.0.0:5000 --workers=2 app:app --reload

19. To run Celery, run the below command under src directory

    celery -A app.celery worker

Visit following links for more information:

https://code.visualstudio.com/docs/devcontainers/containers

https://code4it.dev/blog/run-postgresql-with-docker/

https://medium.com/idomongodb/installing-redis-server-using-docker-container-453c3cfffbdf

https://saggu.medium.com/how-to-connect-nultiple-docker-conatiners-17f7ca72e67f

If CORS error is encountered during development, visit following link:

https://medium.com/@dtkatz/3-ways-to-fix-the-cors-error-and-how-access-control-allow-origin-works-d97d55946d9