BioCheck (bio-compose-server): A Biological Simulation Verification Service

This service utilizes separate containers for REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance.

Getting Started:

**The REST API can be accessed via Swagger UI here: https://biochecknet.biosimulations.org/docs

FOR DEVELOPERS:

This application (bio_check) uses a microservices architecture which presents the following libraries:

• compose_api: This library handles all requests including saving uploaded files, pending job creation, fetching results, and contains the user-facing endpoints.
• storage: This library handles MongoDB configs as well as bucket-like storages for uploaded files.
• compose_worker: This library handles all job processing tasks for verification services such as job status adjustment, job retrieval, and comparison execution.

The installation process is outlined as follows:

1. git clone https://github.com/biosimulators/bio-check.git

2. cd assets

3. touch .env_dev

4. Enter the following fields into the .env_dev file:

    MONGO_URI=<uri of your mongo instance. In this case we use the standard mongodb image with the app name bio-check>
    GOOGLE_APPLICATION_CREDENTIALS=<path to your gcloud credentials .json file. Contact us for access>
    BUCKET_NAME=bio-check-requests-1  # name of the bucket used in this app
   

5. Pull the and run the latest version of Mongo from the Docker Hub. (docker run -d -it mongo:latest or similar.)

Notes:

• This application currently uses MongoDB as the database store in which jobs are read/written. Database access is given to both the compose_api and compose_worker libraries. Such database access is executed/implemented with the use of a Supervisor singleton.