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EXCEL to FHIR

A typescript package to convert spreadsheet (EXCEL) to FHIR resources in JSON.

The workflow is as follows:

  • convert format: read the spreadsheet and convert it to JSON
  • transform schema: transform the JSON using JSONATA to FHIR resources (JSON)

We use JSONATA to transform schemas with mapping rules defined in a .jsonata file.

This package aims to transform GameBus Excel to FHIR R4 (ConceptMap) resources, for which the mapping rules have been defined in this folder. If there are changes on GameBus Excel schema (e.g. changes on sheets and colomns), the mapping rules must be updated accordingly. An example of the GameBus Excel file is provided as gamebus.xlsx.

Requirements

If you have deno installed, it's a good practice to update it to lastest version using the command: deno upgrade.

Usage

Run the typescript package directly:

# run conversion
deno run --allow-read --allow-write https://raw.githubusercontent.com/nwo-strap/excel-to-fhir/main/excel-to-fhir.ts -f example-excel.xlsx -s sheetname1 sheetname2 -j mapping1.jsonata mapping2.jsonata

# show help
deno run --allow-read --allow-write https://raw.githubusercontent.com/nwo-strap/excel-to-fhir/main/excel-to-fhir.ts -h

Run the typescript package as a command line tool

If you want to install the package as CLI tool and run:

# install
deno install --allow-read --allow-write https://raw.githubusercontent.com/nwo-strap/excel-to-fhir/main/excel-to-fhir.ts

# run conversion
excel-to-fhir -f example-excel.xlsx -s sheetname1 sheetname2 -j mapping1.jsonata mapping2.jsonata

# show help
excel-to-fhir --help

Use Deno tasks in repo

You can define Deno tasks in the deno.json file with specific inputs and options.

In the file you can find the task transform, which is defined to convert gamebus.xlsx file to FHIR resources with all valid sheets (with all corresponding jsonata files). You can run the conversion with the following command:

# clone the repo
git clone https://github.com/nwo-strap/excel-to-fhir.git
cd excel-to-fhir

# run the task
deno task transform

Development

To run unit tests, use the following command:

deno test --allow-read --allow-write

To watch file changes and check output during development, use the following command:

deno task dev