An example HPDS environment load with a subset of the NHANES data.
NOTE : This repository uses docker-compose and Docker. Please make sure your Docker and docker-compose are up to date before trying to run anything.
This repository serves as an example load of phenotype data into HPDS and a Jupyter Notebook test environment for working with that data.
This environment provides an incomplete infrastructure that is good for adapting your data into a source form that can be loaded in PIC-SURE-HPDS and for validating your load of that data. To complete this environment and make it production ready, you must put the HPDS instance behind a properly configured PIC-SURE API v2 instance.
The repository has 2 folders in it:
nhanes-load-example: This is an example load process for PIC-SURE-HPDS from a gzipped CSV file which is a subset of the NHANES database.
jupyter-notebooks: Some Jupyter Notebook examples that show statistics for each of the concepts in the dataset.
To run the example you need a docker environment with docker-compose configured. We assume you are on a Linux based environment. We strongly recommend that you use docker-machine if you are in a non-linux environment such as Windows or Mac.
Start by following the instructions in nhanes-load-example/README.md
Once that completes successfully, start the stack from this folder:
docker-compose up -d
Then open your web browser while pointing at your docker-machine, docker engine host, or localhost if you are just running it locally.