FAIDARE: FAIR Data-finder for Agronomic Research

This application provides web services (based on the BrAPI standard) and a web interface with easy to use filters to facilitates the access to plant datasets from a federation of sources.

How to contribute

Look at the contribution guide.

Install development environment

• Install node and npm

Installation via nvm is recommended for easier control of installed version: https://github.com/creationix/nvm

nvm install 10.13.0
nvm use v10.13.0

• Install Angular CLI

npm install -g @angular/cli@7.0.6

• Install JS dependencies

cd frontend
npm install

• Install latest Java JDK8

See latest instructions for your operating system.

• (Optional) Install docker and docker-compose

If you want to run an Elasticsearch and Kibana instance on your machine. You can use your favorite package manager for that

Run backend development server

First make sure you have access to an Elasticsearch HTTP API server on http://127.0.0.1:9200 (either via ssh tunneling or by running a local server).

If you want to run an Elasticsearch server on your development machine you can use the docker/docker-compose configuration like so:

docker-compose up

This will launch an Elasticsearch server (with port forwarding 9200) and a Kibana server (with port forwarding 5601)

Warning: This repository does not automatically index data into Elasticsearch, you need to prepare your indices beforehand.

If you just need access to API (to run the ng serve on top of it), you can run:

./gradlew bootRun

Otherwise, for the complete server (backend APIs + frontend interface), you can run:

./gradlew assemble && java -jar backend/build/libs/faidare.jar

The server should then be accessible at http://localhost:8380/faidare-dev

Run frontend development server

The frontend requests are redirected to the local backend API server (see instructions above to launch) via the Angular proxy.

You can run the development server with the following command:

cd frontend
ng serve

GitLab CI

When creating merge requests on the ForgeMIA GitLab, the GitLab CI will automatically run the tests of the project (no need to do anything).

If you want to run the GitLab CI locally, you have to follow this steps:

1. Install gitlab-runner
2. Run the following command (with the correct GnpIS security token):

gitlab-runner exec docker test 

Spring Cloud config

On bootstrap, the application will try to connect to a remote Spring Cloud config server to fetch its configuration. The details of this remote server are filled in the bootstrap.yml file. By default, it tries to connect to the remote server on http://localhost:8888 but it can of course be changed, or even configured via the SPRING_CONFIG_URI environment variable.

It will try to fetch the configuration for the application name faidare, and the default profile. If such a configuration is not found, it will then fallback to the local application.yml properties. To avoid running the Spring Cloud config server every time when developing the application, all the properties are still available in application.yml even if they are configured on the remote Spring Cloud server as well.

The configuration is currently only read on startup, meaning the application has to be rebooted if the configuration is changed on the Spring Cloud server. For a dynamic reload without restarting the application, see http://cloud.spring.io/spring-cloud-static/Finchley.SR1/single/spring-cloud.html#refresh-scope to check what has to be changed.

If you want to use a Spring Cloud configuration server, please refer to https://spring.io/guides/gs/centralized-configuration/