README.md

# CSE 5810 Biomedical Informatics (Spring 2022)

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## Implementation Project Final Status
### **Frank Zappulla**
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#### Requirements

- *For Windows Users Only* - [install WSL2](https://www.youtube.com/watch?v=n-J9438Mv-s&t=51s)
    - This will give you a real linux terminal where you can use conda
- Conda 
    - If you don't have Conda, you should install [Miniconda](https://docs.conda.io/en/latest/miniconda.html) instead of Conda
- [Docker](https://docs.docker.com/get-docker/)
    - If you are on a *Windows* machine, you must install [WSL2](https://www.youtube.com/watch?v=n-J9438Mv-s&t=51s) first

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### Getting Started Instructions
1. Start your local instance of [HAPI FHIR](https://github.uconn.edu/frz02001/HAPI_FHIR)
2. clone this repository
    - `git clone https://github.uconn.edu/frz02001/cse5810_implementation.git`
3. Change directory into this repository
    - `cd cse5810_implementation`
4. Create your conda environment using the included yaml file
    - `conda env create --file=hapi_fhir.yaml`
    - You should first alter the `prefix: /home/frank/miniconda3/envs/hapi_fhir` part of the yaml file to reflect your particular conda environment. This will likely be `/home/$USER/miniconda3/envs/hapi_fhir`
5. Activate the conda environment you just created
    - `conda activate hapi_fhir`
6. Launch jupyter lab
    - `jupyter lab`
7. Copy and paste the url in the terminal into your browser
8. Double click on the `hapi_fhir.ipynb` file to open the developer's notebook
9. You should now be using the notebook that was demonstrated during class