National Reef Monitoring Network Data Portal

The National Reef Monitoring Network (NRMN) Data Portal is a web application for collation, validation, and storage of all data obtained during shallow reef surveys conducted by the NRMN. NRMN is a sub-facility of the Integrated Marine Observing System IMOS.

The application consists of the following components:

• A Spring Boot based backend with a REST API
• A React user interface
• A Postgres database

The NRMN Data Portal is deployed at NRMN - Data Portal.

This repository contains the source code for the NRMN application backend, the user interface and DDL code for initialisation of the database.

Licensing

This project is licensed under the terms of the GNU GPLv3 license.

Structure

This repository contains a multi-module maven project used to build both the front-end react application, the backend end spring boot application and the war. The maven project is structured as follows:

Project	Description
.	multi-module maven project containing all sub-modules used to build the project and containing common settings
api	maven sub-module used to build the spring boot backend
web	maven sub-module project used to build the react front-end
app	maven project to assemble the api and web artifacts in a single application WAR
db	SQL scripts containing the data and application DDL and scripts to insert data for testing

Building

Build requires Java 11 with Maven and Node v16 with Yarn v1.x. A Dockerfile is also provided with the necessary prerequisites.

docker build --tag nrmn-builder --build-arg BUILDER_UID=$(id -u) .
docker run -it -v $PWD:/home/builder/src nrmn-builder yarn --cwd src/web
docker run -it -v $PWD:/home/builder/src nrmn-builder mvn -f src clean package

Testing

mvn clean install

Developing

Running in Docker / Podman

The project root contains two Dockerfiles Dockerfile.app and Dockerfile.db for local development, testing and provisioning to a container registry. These same instructions will work for Podman by replacing docker with podman.

Build the application WAR file:

mvn clean package

Build the application and database images:

docker build -t nrmn-app-dev -f Dockerfile.app .
docker build -t nrmn-postgis -f Dockerfile.db .

Create a network to connect the two containers then run up the the database and application. Note that POSTGRES_PASSWORD is used to access the database user postgres and is not used by the application.

docker network create dev-net
 
docker run --name nrmn-postgis-1 --network dev-net -p 5432:5432 -d -e POSTGRES_PASSWORD=5A5qADoVk3 nrmn-postgis
 
docker run --name nrmn-app-dev-1 --network dev-net -p 8080:8080 -d -e POSTGRES_HOST=nrmn-postgis-1 nrmn-app-dev

The web application will now be available at http://localhost:8080.

The application database will be initialised on first load with a basic application schema suitable for development. If this is not sufficient a full database backup may be restored in the usual way through pgAdmin or with pg_restore.

Creating an empty database

This application required PostreSQL 11 + the PostGIS extension. Database connection details specified in application.properties.

Create an empty development database:

sudo su - postgres
createdb nrmn_dev
psql -c "CREATE ROLE nrmn_dev PASSWORD 'nrmn_dev' LOGIN;"
psql -d nrmn_dev -c "CREATE SCHEMA nrmn AUTHORIZATION nrmn_dev;"
psql -d nrmn_dev -c "CREATE EXTENSION postgis;"
exit

Apply the DDL against this database using the following scripts in order:

db/schema/CreateTables.sql
db/schema/CreateMiscAncillaryObjects.sql
db/schema/ApplyConstraints.sql
db/schema/BasicIndexing.sql
db/endpoints/CreatePrivateEndpoints.sql
db/endpoints/CreatePublicEndpoints.sql
db/endpoints/EndpointIndexes.sql

Then add the application tables:

api/src/main/resources/sql/application.sql

Also add any sample data if required:

api/src/test/resources/testdata/FILL_DATA.sql
api/src/test/resources/testdata/FILL_ROLES.sql

Finally run all of the scripts in db/schema-update/ in order.

Developing with Codium / Visual Studio Code

Instructions are based on VSCode v1.66 running on Linux. and assume that Chrome / Chromium is installed.

1. Install the extension Lombok Annotations Support and Extension Pack for Java.
2. Open the nrmn-application repository as a folder
3. Go to Debug & Run and choose App from the list of configurations and start debugging
4. The first time the application is run may take some time as Yarn and Maven will download build dependencies.
5. Verify the debugger is working correctly by adding breakpoints in appropriate places in LoginForm.js and AuthController.java.
6. On Log In both the JS and Java breakpoints should be hit synchronously.

Updating Database Schema

Scripts to modify the database schema are stored in scripts/db-update once applied. Do not modify application.sql. Script names should have the form 00-Script_Description.sql where 00 is incremented for each script and consist of a single update.