Table of contents

• Crop Pest and Disease Data API (AgDxAPI)
  • Background
  • Objectives:
  • Funding
  • Tasks
  • Deliverables
  • Versions
  • Dependencies
  • Tools used
• Development setup
  • Setup IntelliJ
  • Migration
  • API Explorer

Crop Pest and Disease Data API (AgDxAPI)

Background

AgDx is a newly formed alliance initiated by several CGIAR centers, PlantVillage and EDDMaps which are publicly funded, non-profit organizations dedicated to research for development and education in agriculture with the aim to improve plant health globally through ICT tools.

As an alliance of individual platforms, tools and databases aimed at supporting agricultural health in different aspects, AgDx has committed to address these shortcomings through the development of Application Program Interfaces (API's) to facilitate sharing of data between platforms and/or by providing links between complementary ICT tools where appropriate.

To initiate this process, minimum data elements for exchange between alliance databases and applications are determined, and harmonize these with existing data standards and ontologies to develop and document a standardized web service API specification.

Objectives:

Create data exchange standards, and a REST API (dubbed AgDxAPI) for plant pest and disease data held in disparate databases and applications.

Collaboration among a community of developers of pest and disease databases and applications and the CGIAR Platform on Big Data in Agriculture.

It will build on existing data standards for Agriculture, such as the Crop and Agronomy ontologies.

Funding

This research was undertaken as part of, and funded by, the CGIAR Research Program on Roots, Tubes and Bananas (RTB) and supported by CGIAR Trust Fund contributors.

Tasks

1. Review data structures in existing pest and disease databases and applications and recommend a minimum set of data for interoperability and exchange.
2. Participate in requirements gathering via agile methodologies to define functional and non-functional requirements.
3. Review existing data definition standards and ontologies from the CGIAR, Academia, and development organizations like FAO for reuse in defining data exchange attributes for the AgDxAPI.
4. Create a draft version of the AgDxAPI standardized web service API specification for data exchange.
5. Lead the review of the specification in a (virtual) workshop of all stakeholders. The workshop will provide feedback and provide input for the finalization of the first version of the specification.
6. Document the AgDxAPI using widely accepted API documentation standards
7. Develop a demo website showcasing capabilities of AgDxAPI

Deliverables

1. List of minimum data elements suitable for exchange between the pest and disease databases and applications
2. Harmonization of the minimum data elements with existing data standards and ontologies
3. AgDxAPI standardized web service API specification published on the AgDx Alliance Github
4. Documentation of the AgDxAPI including on online API documentation systems such as Apiary and Swagger

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Versions

v0.xx

Version	Status	Release Date	SwaggerHub	Notes
v0.0.1	Development	Feb 04, 2021	LINK
v0.0.2	Development	Jul 13, 2021	LINK

v1.xx

Version	Status	Release Date	SwaggerHub	Notes
v1.0.0	Production	Nov 02, 2021	LINK
v1.0.1	Development	Nov 10, 2021	NA
v1.0.2	Production	Nov 25, 2021	LINK

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Dependencies

• JDK 14

Tools used

• Gradle
• Kotlin

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Development setup

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Setup IntelliJ

Install Spring assistant to help in springboot config processing and code autocompletion Install Spring Assistant option.

Environment variables

To switch the environment in dev mode adjust these basic parameters

SPRING_PROFILES_ACTIVE=dev;DB_URL=jdbc:postgresql://localhost:5432/postgres;DB_USER=user;DB_PASS=pass

Migration

Generate Liquibase changelog file

 ./gradlew migrations:generateChangelog  -PchangeName="Name of Changelog"

example:

 ./gradlew migrations:generateChangelog -PchangeName="Create Users table"

The author defaults to the user currently running the command on the system. Optionally, you can use a different author by adding the -Pauthor argument:

./gradlew migrations:generateChangelog -PchangeName="Create Users table" -Pauthor="The Stig"

Remember to add the changelog file to the changelog.xml file

Generate Swagerjson file

  ./gradlew :api:generateOpenApiDocs

To override default java version without messing with your machine paths and ENV

Create a file in the root of the project gradle.properties

Paste your jDK path org.gradle.java.home=C:\Program Files\OpenJDK\jdk-14.0.2

Change the path according to your JDK installation

API Explorer

Swagger

To explore the api endpoints refer to this LINK.

Apiary

Other tools

generate api HTML

  npm install -g redoc-cli

  redoc-cli bundle -o .\docs\index.html .\docs\agdx.json

generate markdown files

  npm install -g openapi-to-md

  openapi-to-md .\docs\agdx.json > .\docs\API.MD