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

1. Configure environment variables for use only in local development

   • Make a file named .env in the root directory
   • Generate the variables using env.example as a reference
   • 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
     • Echoed into build.env in the set-vars job in gitlab-ci.yml

2. Clone project, make sure virtual environment is installed and activated, and execute the following command:

    pdm sync --dev

3. Run the FastAPI development server:

   pdm run dev

4. Access local server at: http://127.0.0.1:8000

Production Usage

1. Configure CI/CD variables used in production server (main environment) or staging server (staging environment)

   • 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
     • Update the version value in pyproject.toml
     • Also create an entry in the CHANGELOG

   • ROOT_PATH is an optional CI/CD 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 or scheduled pipelines:

     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
     FOREST3D_API_URL	https://my-server.com/doi-api/forest3d/publish-bulk-datacite?is-update=true

2. Merge feature/development branch to main default branch

   • The image related variables can be group variables inherited from the parent group

Forest3D Datasets

The /forest3d/publish-bulk-datacite endpoint bulk publishes Forest3D endpoints to DataCite.

• The metadata for Forest3D datasets are read from an external online JSON file that is set in the CI/CD variable FOREST3D_URL.
• Requires forest3d-key header parameter that matches the value for CI/CD variable FOREST3D_API_KEY.
• Forest3D datasets' doi values must end with a digit to be considered valid.
• Optionally if is-update query parameter is true then updates existing Forest3D datasets in DataCite (if the metadata_modified date is within the last 30 days.)
• The GitLab scheduled pipeline executes every 24 hours and requires that the CI/CD variable FOREST3D_API_URL is set for the corresponding server/environment.

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

Authors

The following employees of the Swiss Federal Institute for Forest, Snow and Landscape Research WSL:

• Ranita Pal
• Rebecca Buchholz
• Sam Woodcock

License

MIT License