Set up the RareLink Framework

Getting Started

Follow these steps to set up the project locally and run tests.

1. Clone the repository:

git clone https://github.com/BIH-CEI/rarelink.git
cd rarelink

2. Create a virtual environment:

python3 -m venv .venv
source .venv/bin/activate  # On macOS/Linux
.venv\Scripts\activate     # On Windows

3. Install RareLink:

pip install rarelink

This installs everything needed for REDCap interaction, Phenopacket export, and the RareLink CLI.

For optional features, install the relevant extras:

pip install rarelink[fhir]    # adds Docker SDK for the toFHIR pipeline
pip install rarelink[data]    # adds numpy and pandas for tabular data processing

For development (includes testing, docs, and all optional extras):

pip install -e .[dev]

4. Configure all api keys necessary to use rarelink by running the following command:

rarelink setup keys

This command will prompt you to enter the following keys:
- BioPortal API key
- REDCap API key
- REDCap URL
- REDCap project ID

Note

You can create your free BioPortal account here: BioPortal

5. Run tests:

pip install rarelink[test]
pytest

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RareLink Framework CLI config

Use the following commands to update the framework and its components, view its status or reset the framework. See RareLink CLI for more information.

rarelink framework --help
rarelink framework update
rarelink framework status
rarelink framework reset

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Import Mapper Configuration

Via the RareLink CLI type:

to be implemented

This command guides you through setting up the Import Mapper pipeline for RareLink. You will be prompted to enter: - Your location of your local (tabular) database. - Your REDCap project URL and API token. - Your location where to store the Import Mapper configurations.

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Phenopacket Pipeline Configuration

The Phenopacket export pipeline requires a BioPortal API key and a CREATED_BY value, both configured via:

rarelink setup keys

Once configured, export Phenopackets with:

rarelink phenopackets export --help

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FHIR Pipeline Configuration

Note

The FHIR pipeline requires the fhir extra: pip install rarelink[fhir]

rarelink fhir setup

This command guides you through setting up the FHIR pipeline for RareLink. You will be prompted to enter:

• Your FHIR server URL.

• If required, your FHIR server username & password.

Note

All sensitive information will also be stored in the hidden configuration file.