fhir-cli 0.6.0

DBTonFhir cli

DBTonFHIR

Description

The goal is to be able to map from a given source to a FHIR server without the help of a gui leveraging existing tools such as git and DBT.

Project template repository

dbtonfhir-template

Setup and installation

Prerequisites

• Python 3.9+

Base setup

• Create an .env file and specify your own configuration (you can copy .env.template and customize)

python3 -m venv .venv
source .venv/bin/activate
pip install --upgrade pip
pip install -r requirements/tests.txt
pre-commit install 

IntelliJ/Pycharm setup

Install the ProjectEnv plugin to load environment variables from your .env file

Fhir Cli

Install

make install 

Build package

make build

Usage

fhir --help

OMOP

Vocabulary

• Download vocabularies at https://athena.ohdsi.org/
• Create a vocabulary folder and extract the files there

CDM 5.4

To build the OMOP CDM 5.4 schema in your target database, execute the following files in this order:

1. OMOPCDM_postgresql_5.4_ddl.sql
2. OMOPCDM_postgresql_5.4_primary_keys.sql
3. vocabulary.sql
4. OMOPCDM_postgresql_5.4_constraints.sql
5. OMOPCDM_postgresql_5.4_indices.sql

Tests

Unit tests

make unit-tests

End to end tests

make e2e-tests

Versioning and publishing

This project follows the semver versioning.

To bump the version, edit the version attribute in setup.cfg and add a tag on the main branch with the version prefixed with a v (eg. v0.1.0). Be careful to tag with the same version specified in setup.cfg.

git tag v0.1.0
git push --tags

As soon as the tag is pushed, a package will be built and published to Pypi.

Implementation