DBTonFhir cli
Project description
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
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
Vscode setup
Configure your environment
In .vscode/settings.json
, add your environment variables as such
{
"terminal.integrated.env.linux": {
"DBT_PROFILES_DIR": "."
},
"terminal.integrated.env.osx": {
"DBT_PROFILES_DIR": "."
},
"terminal.integrated.env.windows": {
"DBT_PROFILES_DIR": "."
}
}
IntelliJ/Pycharm setup
Configure your environment
Add the DBT_PROFILE_DIR
environment variable to your shell environment
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:
OMOPCDM_postgresql_5.4_ddl.sql
OMOPCDM_postgresql_5.4_primary_keys.sql
vocabulary.sql
OMOPCDM_postgresql_5.4_constraints.sql
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
Project details
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