Simulation Verification Service and API
Project description
BioCheck: A Simulation Verification Service API
This service utilizes separate containers for API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance.
Getting Started:
HIGH-LEVEL bio_check
API:
The primary method of user-facing interaction for this service is done through the use of a high-level "notebook" api called bio_check
. Installation of this tooling
can be performed using PyPI as such:
pip install bio-check
PLEASE NOTE: You must have >=python3.9
in order to use the high-level api.
GOOGLE COLAB DEMO:
A convenient notebook demonstrating the functionality of this service is hosted on Google Colab and can be found here.
FOR DEVELOPERS:
This application (bio_check
) uses a microservices architecture which presents the following libraries:
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.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:
git clone https://github.com/biosimulators/bio-check.git
cd bio-check/bio_check
touch .env
- Enter the following fields into the
.env
file:MONGO_DB_USERNAME, MONGO_DB_PWD, MONGO_DB_URI
. - Ensure that your IP address has been authorized in the
bio-check
cluster in Mongo Atlas.
Notes:
- This application currently uses MongoDB as the database store in which jobs are read/written. Database access is given to both the
api
andworker
libraries. Such database access is executed/implemented with the use of aSupervisor
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.
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