BioStudies Backend Services

Project containing the BioStudies backend services. Below you'll find a description of each main component in the project:

• Bio Admin: Spring boot administration module.

• CI: It contains the definitions of the CI/CD GitLab jobs as well as the required scripts.

• Client: Contains the web client used to interact with the submitter and the code for the BioStudies CLI

• Commons: Contains common functionality used in all modules like the model definition, serialization, utils, etc.

• Infrastructure: Contains infrastructure related tooling to help deploying the application

• Scheduler: Module that contains scheduled task to perform BioStudies related processes like submissions export to the UI or Europe-PMC submissions processing.

• Submission: Contains all the services that are specifically related to the submissions.

Deploying The Submitter WebApp

This section will explain how to deploy a local instance of the submitter webapp from scratch. You'll need to have:

• Gradle
• Java (at least 8 version)
• Docker

Database Setup

Execute the command gradle setUpTestDatabase in the infrastructure folder. This will deploy a custom MySql image loaded with the application's schema and some initial test data and the following configuration:

• Container name: biostudies-mysql
• User: root
• Password: admin
• Port: 3306

RabbitMQ Setup

Execute the command gradle setUpRabbitMQ in the infrastructure folder. This will deploy a RabbitMQ image with the following configuration:

• Container name: biostudies-rabbitmq
• User: manager
• Password: manager-local
• Port: 5672
• Admin console: http://localhost:15672

FireMock Setup (EBI only)

• Generate a GitLab access token here with at least read_registry scope
• Execute docker login dockerhub.ebi.ac.uk and enter your GitLab username when prompted for username, and the access token when prompted for a password
• Execute gradle setUpFireMock in the infrastructure folder

The steps above will deploy a FIREMock image listening on localhost, with the following configurations

• Container name: biostudies-firemock
• User: user
• Password: pass
• Port: 8092

Configure WebApp

1. Move to Submission WebApp folder
2. Edit the Submission WebApp Config File to match the Local Submission WebApp Config File
3. Choose a folder in your file system to be used as the application storage. It's recommended that this is an empty folder for fresh instances. Set this folder path in the basepath property of the configuration file
4. Execute the command gradle bootRun

Note: In order for the messages in the rabbit queues to be processed you need to start the Handlers application

Make A Submission

In order to make a submission, you can use the BioStudies CLI. Find more information here.

Page Tab

Page tab is the specification used to define studies in BioStudies. In order to get a better understanding you can refer to:

• Page Tab Specification
• All In One Example
• File List Example

Development Process

In this section there're useful documents related to the development process

• Coding Conventions