FHIR for Research

The content in this repository is under active development. Please proceed with caution.

GitHub Actions automatically builds commits to the main branch to https://nih-odss.github.io/fhir-for-research/.

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Dependencies

• Quarto
• R
• Jupyter and Python3 (if you use embedded Python)

Python uses venv (https://quarto.org/docs/projects/virtual-environments.html):

You will need to create a venv in python_env/:

python3 -m venv python_env

Then run source python_env/bin/activate to activate the venv, and the following command to install dependencies:

pip install -r requirements.txt

If you add a dependency, run pip freeze > requirements.txt to update the requirements file.

Better git support for Jupyter Notebooks is provided by nbdime and configured via the .gitattributes file. For more information, see here.

Quick start

• Clone this repository
• Run quarto preview (this will compile everything, start a local web server, and launch web browser to show the content form the server)

Checking for broken links

This website contains a number of links to external websites. To identify broken links, the linkchecker can be used:

linkchecker https://mitre.github.io/fhir-for-research/

To use a custom SSL certificate chain, modify ~/.config/linkchecker/linkcheckerrc to set sslverify to the path of the .crt file.

Checking for orphan pages

Orphan pages are standalone pages on a website that have no links leading to them from other parts of the site. Essentially, without the direct URL, a user cannot find these pages. In addition, because search engine crawlers depend on following links from one page to another to index a site, they usually can't discover and index these orphan pages.

To identify them, run the following command:

python scripts/find_orphan_pages.py

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License

Copyright 2023 The MITRE Corporation

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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MITRE: Approved for Public Release / Case #23-0966