envidat / doi-publishing-api

FastAPI server for publishing to DataCite.

doi-publishing-api

Microservice API to publish DOIs on Datacite.

View the API docs

Email

This service works in tandem with the email relay server Catapulte.

The EnviDat email microservice can be found here.

Development Usage

Environment Variables

1. Make a file named .env in the root directory

2. Generate the variables using env.example as a reference

3. New environment variables must be added to:

   • env.example because this file is used for validation
   • environment section of the doi-api containers in the docker-compose.<branch>.yml files

Option 1: Docker

1. Run the docker container:

docker compose up  -f <docker compose file> -d

The image should pull, or fallback to building.

Option 2: Standalone

1. Install dependencies:

pip install virtualenv
python -m venv <virtual-environment-name>
   or
Create a virtual environment with PyCharm

<virtual-environment-name>\Scripts\activate
pip install -r requirements.txt

2. Run the FastAPI server directly with PDM:

uvicorn app.main:app --host 0.0.0.0 --port 8000 --reload

3. Access at: http://127.0.0.1:8000

Production Usage

1. Configure environment variables used in production

   • Create individual CI/CD variables for each variable listed in env.example

   • APP_VERSION must be incremented so that a new image is built and the application includes the updated code

     • Create a git tag for the commit that corresponds to the APP_VERSION

   • ROOT_PATH is an optional environment variable and should only be used to if the application uses a proxy

     • Be sure to include a / before the ROOT_PATH value
     • Example configuration: ROOT_PATH=/doi-api
     • Click here for the FastAPI documentation about using a proxy server

   • Create individual CI/CD variables for each the following variables (apart from the ones in env.example) that are used for deployment:

     Key	Example Value
     APP_VERSION	1.1.2
     ROOT_PATH	""
     INTERNAL_REG	registry-gitlab.org.ch/orgname
     EXTERNAL_REG	docker.io
     NGINX_IMG_TAG	1.25
     PYTHON_IMG_TAG	3.10
     DEPLOY_HOSTNAME	server.wsl.ch
     DEPLOY_SSH_KEY	encryption private key
     DEPLOY_SSH_USER	test_user

2. Merge feature/development branch to main default branch

   • The main branch has a pipeline set up in .gitlab-ci.yml that automatically deploys changes to production server
   • The pipeline also requires CI/CD variables that are used to that are used to build and register a Docker image of the application: IMAGE_REGISTRY_USER and IMAGE_REGISTRY_PASS
     • The image related variables can be group variables inherited from the parent group

Pre-commit hooks

• To run the pre-commit hooks manually open app in terminal and execute: pre-commit run --all-files
• These hooks ensure that the application uses standard stylistic conventions
• To view or alter the pre-commit hooks see: .pre-commit-config.yaml

Tests

• Tests are located in tests
• To run tests manually open app in terminal and execute: pytest

Scripts

• Scripts are located in the scripts directory

Authors

Ranita Pal, Swiss Federal Institute for Forest, Snow and Landscape Research WSL
Rebecca Kurup Buchholz, Swiss Federal Institute for Forest, Snow and Landscape Research WSL
Sam Woodcock, Swiss Federal Institute for Forest, Snow and Landscape Research WSL

License

MIT License