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Open Source Science

https://github.com/cdcgov/fhirsheets

https://github.com/cdcgov/fhirsheets

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
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    Found codemeta.json file
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    Found .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (9.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: CDCgov
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 803 KB
Statistics
  • Stars: 2
  • Watchers: 4
  • Forks: 3
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

FHIRSheets

FhirSheetsiIs a command-line tool that reads an Excel file in FHIR cohort format and generates FHIR bundle JSON files from it. Each row in the template Excel file is used to create an individual JSON file, outputting them to a specified folder.

Table of Contents

Features

  • Reads an Excel file following the FHIR cohort import template.
  • Converts each row in the Excel file to a FHIR bundle JSON file.
  • Exports generated JSON files to a specified output folder.

Requirements

  • Python 3.x
  • Required Python packages (see requirements.txt)

Installation

  1. Clone this repository: ```bash git clone https://github.com/CDCgov/synthetic-data.git cd fhir-python-cohort-generation
  2. Install the required packages: ```bash pip install -r requirements.txt ## Usage

  3. Fill Out the Template:

    • Open the template file src/resources/Fhir_Cohort_Import_Template.xlsx.
    • Fill out each row with the relevant data.

  4. Run the Tool:

    • Use the python -m src.cli.fhirsheets module script with the required arguments:
      • --input-file: The path to the input Excel file.
      • --output-folder: The path to the output folder where the JSON files will be saved.

```bash python fhirsheets.py --input src/resources/FhirCohortImport_Template.xlsx --output /path/to/output/folder 3. The tool will generate one FHIR bundle JSON file for each row defined in the template.

Example

bash python fhirsheets.py --input src/resources/Fhir_Cohort_Import_Template.xlsx --output ./output_bundles In this example, each row in the `Fhir_Cohort_Import_Template.xlsx` file will be processed, and a corresponding JSON file will be generated in the `output_bundles` folder.

License

This project is licensed under the MIT License. See the LICENSE file for more information.

Owner

  • Name: Centers for Disease Control and Prevention
  • Login: CDCgov
  • Kind: organization
  • Email: data@cdc.gov
  • Location: Atlanta, GA

CDC's collaborative software projects to protect America from health, safety, and security threats, both foreign and in the U.S.

GitHub Events

Total
  • Push event: 4
  • Fork event: 3
Last Year
  • Push event: 4
  • Fork event: 3

Dependencies

requirements.txt pypi