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Codebase and Community of Practice for Go.Data (https://goarn.who.int/virtual-spaces/godataproject), an outbreak investigation tool developed by WHO in collaboration with Global Outbreak Alert and Response Network Partners.

Home Page: https://worldhealthorganization.github.io/godata/

License: GNU General Public License v3.0

R 2.60% Python 0.16% Batchfile 0.01% JavaScript 0.34% TSQL 0.03% HTML 96.87% CSS 0.01%
interoperability dhis2 covid19 data-management r-analytics reporting-infrastructure godata analytics

godata's Introduction

Welcome to the Go.Data Site!

This repository serves as an umbrella site to gear the community towards existing technical documentation, resources, and open source components developed by and for the Go.Data community worldwide, particularly in the area of Analytics and Interoperability.

You can find all additional repos connected to the Go.Data tool in the overarching WHO Github Repository by filtering for topics = "go-data", as seen here.

What is Go.Data?

Go.Data is a software for contact tracing and outbreak response developed by WHO in collaboration with partners in the Global Outbreak Alert and Response Network (GOARN). Go.Data focuses on case and contact data including laboratory data, hospitalizaton and other variables collected through investigation forms that can be configured across settings and disease types. It generates contact follow-up lists and viusalisation of chains of tranmission. It is currently in use in over 60 countries / territories, and in over 80 different institutions at the national or subnational level.

Components

Go.Data utilizes of the following tools and components:

Tool/Component Description Project Repository
Go.Data Installer Creates installers for various system configurations GoDataSource-Installers
Mobile App IOS and Android applications of Go.Data. GoDataSource-MobileApp
Push Notification Server For wiping data from mobile devices. The feature can only be accessed if the required permissions are enabled. GoDataSource_PushNotificationServer
Front End Application The web user interface part of Go.Data. GoDataSource-FrontEnd
Go.Data API The backend of Go.Data that connects to the database, retrieves data etc. GoDataSource-API

In the Go.Data Docs Site, you can find:

Go.Data Analytics Scripts

Example scripts and resources for extracting, cleaning, and running analyses. Output includes dashboards displaying operational performance metrics for contact tracing by contact tracing supervisor and teams.

Go.Data Interoperability Use Cases

We've compiled existing integrations that partners and users have developed, and guidances on if you are considering connecting Go.Data to other system(s).

Go.Data API Documentation

How to work with the Go.Data API, and links to further resources.

How can I contribute?

We would appreciate your contributions or feedback so that the user base can benefit from your experience.

If you have a contribution to make, please email [email protected] to be added to the repository and submit a pull request, including a documentation page on your Use Case for Analytics or Interoperability.

You can also visit our Community of Practice website to swap learnings or post queries at https://goarn.who.int/virtual-spaces/godataproject.

Terms of Use

Please read these Terms of Use and Software License Agreement (the “Agreement”) carefully before installing the Go.Data Software (the “Software”).

By installing and/or using the Software, you (the “Licensee”) accept all terms, conditions, and requirements of the Agreement.

1. Components of the Software

The Software is a product published by WHO (the “Software”) and enables you to input, upload and view your data (the “Data”).

This Agreement governs your use of the Software you have downloaded.

2. Third-party software

2.1. Third-party software embedded in the Software.

The Software contains third party open source software components, issued under various open source licenses:

  • 0BSD
  • AFL-2.1
  • BSD-3-Clause
  • BSD-2-Clause
  • BSD-3-Clause-Clear
  • Apache-2.0
  • MIT
  • MIT-0
  • MPL-2.0
  • CC-BY-3.0
  • CC-BY-4.0
  • CC0-1.0
  • ISC
  • Unlicense
  • WTFPL
  • AGPL-3.0
  • Python-2.0
  • BlueOak-1.0.0
  • Artistic-2.0
  • Zlib
  • Ruby

The text of the respective licenses can be found in Annex 2.

2.2. WHO disclaimers for third-party software.

WHO makes no warranties whatsoever, and specifically disclaims any and all warranties, express or implied, that either of the third-party components are free of defects, virus free, able to operate on an uninterrupted basis, merchantable, fit for a particular purpose, accurate, non-infringing or appropriate for your technical system.

2.3. No WHO endorsement of third-party software.

The use of the third-party Components or other third-party software does not imply that these products are endorsed or recommended by WHO in preference to others of a similar nature.

3. License and Terms of Use for the Software

Copyright and license.

The Software is copyright (©) World Health Organization, 2018, and is distributed under the terms of the GNU General Public License version 3 (GPL-3.0). The full license text of the GNU GPL-3.0 can be found below in Annex 1.

4. Copyright, Disclaimer and Terms of Use for the Maps

4.1.

The boundaries and names shown and the designations used on the maps [embedded in the Software] (the “Maps”) do not imply the expression of any opinion whatsoever on the part of WHO concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted and dashed lines on maps represent approximate border lines for which there may not yet be full agreement.

4.2.

Unlike the Software, WHO is not publishing the Maps under the terms of the GNU GPL-3.0. The Maps are not based on “R”, they are an independent and separate work from the Software, and not intended to be distributed as “part of a whole” with the Software.

5. Acknowledgment and Use of WHO Name and Emblem

You shall not state or imply that results from the Software are WHO’s products, opinion, or statements. Further, you shall not (i) in connection with your use of the Software, state or imply that WHO endorses or is affiliated with you or your use of the Software, the Software, the Maps, or that WHO endorses any entity, organization, company, or product, or (ii) use the name or emblem of WHO in any way. All requests to use the WHO name and/or emblem require advance written approval of WHO.

6. Dispute Resolution

Any matter relating to the interpretation or application of this Agreement which is not covered by its terms shall be resolved by reference to Swiss law. Any dispute relating to the interpretation or application of this Agreement shall, unless amicably settled, be subject to conciliation. In the event of failure of the latter, the dispute shall be settled by arbitration. The arbitration shall be conducted in accordance with the modalities to be agreed upon by the parties or, in the absence of agreement, in accordance with the UNCITRAL Arbitration Rules. The parties shall accept the arbitral award as final.

7. Privileges and Immunities of WHO

Nothing contained herein or in any license or terms of use related to the subject matter herein (including, without limitation, the GNU General Public License version 3 mentioned in paragraph 3.1 above) shall be construed as a waiver of any of the privileges and immunities enjoyed by the World Health Organization under national or international law, and/or as submitting the World Health Organization to any national jurisdiction.

Annex 1

Annex 2

godata's People

Contributors

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godata's Issues

Add list of godata components and links to repositories to readme

Having a list of GoData components in the readme file would be useful for people looking for a more technical understanding of GoData and its components. Currently, most of the repositories are still private and could be made public at some point in the future.

R Reporting - API Scripts - functions to create loops for batched import of records

To avoid API timeouts, need to adapt scripts to loop through records according to pre-defined chunk sizes.
Example below of rationale:

chunk_size = 10000
data_instance <- pull_data_func()
base_url <- "url"
chunk_num <- 0
dat_out <- data_instance


while (nrow(data_instance) == chunk_size) {
  
  temp_url <- paste0(base_url, "$skip=chunk_num$limit=", chunk_size)
  data_instance <- get(temp_url)
  data_out <- bind_rows(data_out, data_instance)
  chunk_num <- chunk_num + chunk_size

}

Lab - Technical Documentation for Go.Data Users peforming lab-related analyses or operations

Build out Laboratory page (location to be decided, within overall hierarchy)

  • Technical Overview of Go.Data Lab Module Variables
  • Key Considerations for Lab Module use (incl config of reference data, bulk actions with API of laboratories, etc).
  • How to import Go.Data lab data (incl sample lab import template)
  • How to Export Go.Data lab data (incl sample dummy data export with lab vars)
  • How to Produce analyses with Go.Data lab Data (incl sample use case such as linking to shiny app)

@giovfer

Access Token

When running 01_data_import_api.R in its current format, the access_token variable is not being defined, that is, it stays as 'NULL' despite having correct the right role, username, password, outbreak id and the access token being generated (in the console).

As a result, I'm unable to pull data from Go.Data through R. The exact error I'm getting is Error 401 - Authorization Required

Currently using RStudio Version 1.3.1093 and R x64 4.0.3

@sarahollis maybe you might help on this one?

Select a Platform for Go.Data Community of Practice

The Go.Data community of practice is being transitioned out of the previous community platform. The previous community platform provided a space where community members could:

  • request for demo accounts,
  • ask questions about setting up Go.Data,
  • seek technical support for issues,
  • receive product updates, and
  • share use cases that they were working on

This transition presents an opportunity to set up a robust community platform with established systems and processes for product updates, collaboration, and technical support.

Some potential options for this include; Notion, Discourse, and Discord.

Select and Apply Open Source License for Go.Data

Go.Data is an outbreak investigation tool for data collection during health emergencies. It includes use case functionality for case investigation, contact follow-up, visualization of chains of transmission and is designed for flexibility in the field.

Go.Data is the initiative of a group of public health partners and is managed by the Global Outbreak and Response Network coordinated by WHO.

Go.Data aims to strengthen and enhance technical support to all countries for readiness activities; outbreak risk assessments; field investigations and response, including response research.

Go.Data uses various open source software components and modules with various open source licenses including:

  • MIT
  • GNU AGPL v3.0
  • Apache-2.0
  • WTFPL
  • BSD-2-Clause
  • 0BSD
  • ISC

We would like to select and apply an appropriate open source license that will take into account the existing open source components.

Publish Go.Data Public Product Roadmap

A high level visual that maps out the vision, direction, and evolution of Go.Data over time is an instrumental part of open sourcing Go.Data. Providing the open source community high level details about ongoing work, upcoming features, and issues already resolved empowers them to better plan around their adoption of the software, offer present or future contributions, and manage expectations all around. This also reduces the risk of independent contributors maintaining forks or parallel solutions.

Go.Data's product roadmap is managed internally. This issue proposes making high level product roadmap that is available to the Go.Data open source community. This could be in the form of a GitHub project board with high level descriptions.

R Reporting - Adding raw and clean versions of sample dummy data

Right now only sample data is from vars already cleaned and re-named.
Include instead output raw and clean - raw where names appear as is in .json
This may only include non-list vars, since lists cant be exported - and separate export for list vars
Appended data dictionaries

GIS - Technical Documentation for Go.Data Users performing GIS analyses

Build out GIS page here

  • Technical Overview of Go.Data Location Variables
  • How to Configure Go.Data Locations (incl sample location import template)
  • Key Considerations for Location Config (incl sources for location data
  • How to Export Go.Data Locations (incl sample dummy data export with location vars)
  • How to Produce Maps with Go.Data Location Data (incl sample map product)

@LangsterGA

Broken link to CoP in ReadMe

Bug description

The link to the Go.Data Community is not working - a 403 Error page is shown.

To Reproduce

  1. Go to https://github.com/WorldHealthOrganization/godata?tab=readme-ov-file#how-can-i-contribute
  2. Click on https://community-godata.who.int/
  3. Error page appears

Expected behavior

No error page should appear. Not clear if the link is incorrect on GitHub, or if the web page is down. Suspecting that the correct link to the CoP would be https://goarn.who.int/virtual-spaces/godataproject.

Screenshots

image

Desktop (please complete the following information):

  • Browser: Chrome

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