linuxforhealth-csvtofhir 1.2.0

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

OS X / Linux

# 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 --clear && \
        source venv/bin/activate && \
        python3 -m pip install --upgrade pip setuptools wheel
        
python3 -m pip install -e .[dev]
# run tests
python3 -m pytest

Windows Setup

Launch the Windows Command and "Run as Administrator"

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

# create the virtual environment (may take some time to complete)
python -m venv venv --clear
.\venv\Scripts\activate
python -m pip install --upgrade pip setuptools wheel
# integrate the local development environment with the virtual environment
python -m pip install -e ".[dev]"

The pip install command for the local project will print a WARNING similar to

WARNING: The script csvtofhir.exe is installed in 'C:\Users\someuser\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\LocalCache\local-packages\Python39\Scripts'
which is not on PATH.

Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.

On Windows the csvtofhir CLI is "compiled" as an EXE and resides within a local cache directory. This directory must be on the SYSTEM path in order to invoke csvtofhir without including the full path to the executable.

To execute unit tests, simply run:

python -m pytest

Optimized Streaming Support

Csv To FHIR provides an optimized means of streaming files using smart_open. smart_open supports streaming files from common cloud storage stores (AWS, Azure, GCS) as well as over common transfer protocols such as HTTP, HTTPS, SFTP, HDFS, etc.

To include smart_open, install the optimized-streaming extra

python -m pip install -e ".[optimized-streaming]"

CSVToFHIR CLI

The CLI supports:

DataContract validation

csvtofhir validate -f demo/config/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 demo  -o demo/output

The convert utility creates a separate output directory for each unique patient record.

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 demo/input/patient.csv -c demo/config  -o demo/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.

Optional Notebook Support

CsvToFhir includes optional support for using notebooks and visualization tools such as JupyterLab.

To add notebook support run setup with the "notebook" extra:

python3 -m pip install -e .[notebook]

Use the following commands to launch the notebook server

# Windows Example
jupyter-lab --app_dir=src\ --preferred_dir=notebooks\

# Linux Example
jupyter-lab --app_dir=./src --preferred_dir=./notebooks

Additional Documentation

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