This repository provides software to convert from a ReproSchema protocol into a set of FHIR resources.
git clone git@github.com:kind-lab/reproschema-to-fhir --recursive
cd reproschema-to-fhir
mkdir fhir_output
cp .env.example .env
# create the python environment
conda env create -f environment.yml
pip install -e .
# Edit .env to point to the correct location of the reproschema-library
bash job.sh- Clone this project recursively.
git clone git@github.com:kind-lab/reproschema-to-fhir --recursive- If you've already cloned the repo, you can pull the submodule with
git submodule update --init --recursive
- Create a folder to store the questionnaire you wish to transform from reproschema to FHIR.
- Create a .env file in the directory where you cloned this project. Please see .env.example for reference.
- Create a conda environment using the environment.yml file provided in the repository.
conda env create -f environment.yml
- Install the reproschema_to_fhir Python module
pip install -e .- This is an editable install that symlinks the local files, allowing you to make changes to the code and see the changes reflected immediately.
- Run the main bash script:
./job.shto run all questionnaires or to run the script on an individual questionnaire:python main.py <path of reproschema folder>
Once executed, you should have 3 json files containing the questionnaire resource and their associated valuesets and codesystems in your current directory.
Clone this repository recursively to include the reproschema-library submodule.
git clone git@github.com:kind-lab/reproschema-to-fhir --recursiveconda env create -f environment.yml
pip install -e .We are using reproschema as a submodule. To add reproschema as a submodule, the following commands were run in the main directory of this project:
git submodule add https://github.com/ReproNim/reproschema-library/ reproschema-library
cd reproschema-library
git checkout 43e7afab312596708c0ad4dfd45b69c8904088ae
cd ..