linuxforhealth-csvtofhir 1.0.0

Maps and converts delimited data to FHIR resources.

CSV to FHIR

Loads CSV records from file, and maps them to FHIR resources.

Pre-requisites

• Python >= 3.9 for application development

Quickstart CLI

# clone the repo
git clone https://github.com/LinuxForHealth/CsvToFHIR.git
cd csvtofhir

# create virtual environment and create an "editable" install
python3 -m venv venv && source venv/bin/activate && python3 -m pip install --upgrade pip setuptools
python3 -m pip install -e .[dev]
# run tests
python3 -m pytest

The CSVToFHIR CLI supports:

DataContract validation

csvtofhir% csvtofhir validate -f tests/resources/data-contract/data-contract.json

CSV Conversion

The csvtofhir convert command has two processing modes, directory mode, -d, and file mode, -f.

Directory Mode

In directory mode the convert command is given a base directory path which contains the following subdirectories:

• input: where input, or source, data records are located
• config: where the CSVToFHIR data contract configuration, data-contract.json, and supporting files are located.

The -o parameter is used to specify the location where output files are saved.

csvtofhir convert -d /data/csv-data  -o /data/output

File Mode

In file mode the convert command is provided a single file path to convert. The -f flag is used to specify the input data file. The -c flag is used to specify the configuration directory. The -o flag is used in the same manner as directory mode.

csvtofhir convert -f /data/csv-data/Patient.csv -c /data/config  -o /data/output

Code Formatting

CSVToFHIR uses flake8 for style checking and autopep8 for formatting. Flake8 is used to find and identify issues, while AutoPep8 will fix (most of) them.

A simplified workflow to ensure uniform formatting is to . . .

Run AutoPep8 against the source and test code

python3 -m autopep8 src/ tests/ --in-place

And then use Flake8 to find remaining issues, which will need to be manually addressed.

python3 -m flake8 src/ tests/

Flake8 and AutoPep8 are configured using setup.cfg within the flake8 section.

In VS Code to format in the editor, - in-place must be removed from the configuration.

Logging

CSVToFHIR follows best practices for logging configuration. Specifically, the only handler supported is the NullHandler. This allows consuming applications and services to configure handlers as appropriate.

The following table lists packages which emit logging information.

Packages	Description
csvtofhir	CSVToFHIR converter entry point
csvtofhir.fhirrs	Converts CSV source records to FHIR Resources
csvtofhir.pipeline	Pipeline tasks used to align source data with internal CSV models

To utilize logging within a local development environment, please review the comments within the support module.

Additional Documentation

• DataContract Design
• Implementation Guide
• Internal Format Guide
• IDE Configuration