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https://github.com/cdcgov/artemis

An application to assist Utah CDC's Newborn Screening Program

https://github.com/cdcgov/artemis

Science Score: 13.0%

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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    DOI references
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    Scientific vocabulary similarity
    Low similarity (9.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

An application to assist Utah CDC's Newborn Screening Program

Basic Info
  • Host: GitHub
  • Owner: CDCgov
  • License: other
  • Language: Ruby
  • Default Branch: master
  • Size: 7.01 MB
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 4
  • Open Issues: 0
  • Releases: 0
Created over 8 years ago · Last pushed almost 8 years ago
Metadata Files
Readme Contributing License Code of conduct

README.md

Newborn Screening Data on FHIR

Background

The Utah Newborn Screening Program collects a variety of demographic data from the screening specimen that is sent in for a newborn. Often the data collected is missing or inaccurate. In order to complete the data and/or ensure accuracy, the Utah Newborn Screening Program compares this data against the Utah Office of Vital Records and Statistics data from birth and death certificates. The current process is antiquated and would benefit from the usage of a newer technology like FHIR. The full specification can be retrieved here.

This application provides an FHIR interface to compare the data between the Utah Newborn Screening Program and the Utah Office of Vital Records and Statistics.

How To Run

  1. Ensure the correct versions of Docker and Docker Compose are installed per the dependencies.
  2. Run docker-compose up.
  3. The application is at http://localhost:3000
  4. The associated FHIR instance is available at http://localhost:8080

How To Deploy

The main Rails application can be deployed as a containerized application. The application can be configured with the following environment variables:

| Variable | Description | |---------------------------|--------------------------------------------------| | DATABASE_URL | URL to PostgreSQL database. See: database.yml | | FHIR_URL | URL to FHIR server. | | RAILS_ENV | Environment. Recommended: production | | RAILS_RELATIVE_URL_ROOT | Deploy to a relative root. Example: /app |

How To Set Up For Native (Local) Development

  1. Ensure all the dependencies are installed.
  2. Run bin/setup.
  3. Run bin/rails server.

How To Test

  1. Ensure all the dependencies are installed.
  2. Run bin/test.

How To Upgrade Packages

  • For JavaScript packages, run yarn add some_package@1.2.3.
  • For Ruby gems, run bundle update some_package.
  • Ensure that the respective .lock files are updated and added to source control.

Dependencies

This is a Rails v5.1.4 application that requires:

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
  • Fork event: 2
Last Year
  • Fork event: 2

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Dependencies

Dockerfile docker
  • ruby 2.4.2-alpine3.6 build
docker-compose.yml docker
  • jtmille3/hapi-fhir-dstu3-v2.5-postgres latest
  • postgres 9.6-alpine
package.json npm
  • markdown-pdf ^8.0.0 development
  • webpack-dev-server ^2.9.3 development
  • @rails/webpacker ^3.0.2
  • coffeescript 1.12.7
  • lodash ^4.17.4
yarn.lock npm
  • 867 dependencies
Gemfile rubygems
  • annotate >= 0 development
  • better_errors >= 0 development
  • binding_of_caller >= 0 development
  • listen >= 3.0.5, < 3.2 development
  • pry-rails >= 0 development
  • rspec-rails ~> 3.7 development
  • rubocop >= 0 development
  • simplecov >= 0 development
  • simplecov-console >= 0 development
  • simplecov-rcov >= 0 development
  • spring >= 0 development
  • spring-watcher-listen ~> 2.0.0 development
  • web-console >= 3.3.0 development
  • active_hash ~> 1.5.2
  • fhir_client ~> 3
  • jbuilder ~> 2.5
  • pg ~> 0.18
  • puma ~> 3.7
  • rails ~> 5.1.4
  • sass-rails ~> 5.0
  • turbolinks ~> 5
  • uglifier >= 1.3.0
  • webpacker ~> 3.0.2
Gemfile.lock rubygems
  • 110 dependencies