Software Observatory API

This repository contains the source code of the Software Observatory API. This API is a FastAPI application that uses a remote mongodb database.

Development

To start the development environment, first create a virtual environment and install the dependencies:

python3 -m venv venv source venv/bin/activate pip install -r requirements.txt

Then, start the development server:

export CONFIG_PATH=./api-variables/config_db.ini python3 main.py

The API will be available at http://localhost:3500.

Versioning

When a push is done to the main branch, the version of the API should be updated. This is done by adding the new version to VERSION. A GitHub action will create a tag with the version to the version in VERSION file, build and publish the docker image.

Collections

Most endpoints use the observatory.tools collection. The endpoint GET "/tools/names_type_labels" uses the collection observatory.tools_discoverer_w_index. This is due to this collection being processed to contain information of types and labels in a more convenient way.

Mappings

| bioschema | UI | | --------- | ------ | | @type | type | | schema:applicationSubcategory | topics | | schema:additionalType | type | | schema:name | name | | schema:url | webpages | | schema:description | description | | schema:applicationCategory | type | | schema:operatingSystem | os | | schema:license | license | | schema:author | authors | | schema:maintainer | authors | | schema:softwareVersion | version | | schema:codeRepository | repository | schema:featureList | operations | | schema:input | input | | schema:output | output | | schema:downloadURL | download | | schema:softwareHelp | documentation | | schema:citation | publication | | schema:requirements | dependencies | | schema:isAccessibleForFree | registration_not_manadatory | | schema:dateModified | - | | @context | - |

API Documentation

The API documentation is available at https://observatory.openebench.bsc.es/api/docs.

This documentation is automatically generated by FastAPI and is based on the OpenAPI standard.

Production

The API is deployed in the BSC's infrastructure. The deployment is done using docker and docker-compose.

The docker image is built as part of the CI/CD pipeline. It is triggered by pushing a tag to the repository.

Notice that the API is accessible at a subdomain of the OpenEBench platform. The API is available at https://observatory.openebench.bsc.es/api. In development, the API is available directly at http://localhost:3500.

License

This software is licensed under the MIT License. For more information, read the LICENSE file.