diff --git a/README.md b/README.md index 832eabacc..778f50b45 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,12 @@   -# BioCheck: A Biological Simulation Verification Service +# 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: -### **HIGH-LEVEL `bio_check` API:** +#### **The REST API can be accessed via Swagger UI here: [https://biochecknet.biosimulations.org/docs](https://biochecknet.biosimulations.org/docs) -The primary method of user-facing interaction for this service is done through the use of a high-level "notebook" api called `bio_check`. -A convenient notebook demonstrating the functionality of this service is hosted on Google Colab and can be accessed by clicking the above "Open In Colab" badge. - -[View the template notebook as markdown](docs/verification_api_demo.md) - - -Installation of this tooling can be performed using PyPI as such: - -```bash -pip install bio-check -``` - -**PLEASE NOTE: You must have `>=python3.9` in order to use the high-level api.** - -#### Alternatively, **the REST API can be accessed via Swagger UI here: [https://biochecknet.biosimulations.org/docs](https://biochecknet.biosimulations.org/docs) ### **FOR DEVELOPERS:** This application (`bio_check`) uses a microservices architecture which presents the following libraries: @@ -33,22 +18,18 @@ This application (`bio_check`) uses a microservices architecture which presents The installation process is outlined as follows: 1. `git clone https://github.com/biosimulators/bio-check.git` -2. `cd bio-check/bio_check` -3. `touch .env` -4. Enter the following fields into the `.env` file: +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. **Ensure that your IP address has been authorized in the `bio-check` cluster within Mongo Atlas.** +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 `api` and `worker` libraries. Such database access is +- 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. - -### **Note (05/22/2024):** -The only package source that is currently supported by this tooling is `PyPI`. The support of other potential -package sources such as `conda`, `brew`, `apt`, and more is currently under development.