ArboDat+

Overview

ArboDat+ is the continued development of the archaeobotanical database program ArboDat. It is being carried out as a collaborative project between NFDI for Objects, Kiel University, and the Lower Saxony Institute for Historical Coastal Research, Germany.

ArboDat+ is designed as an operating system-independent web application, which can be run in almost any modern browser on most computers. It features a newly implemented PostgreSQL database that transitions the system to an open and free platform. While the database remains relational, data integrity is ensured by adapting the old schema in accordance with the principles of the third normal form.

ArboDat+ uses central lists of standardized vocabularies and thesauri, stored at Dante VZG. It also allows the addition of local attribute labels to the central Dante Server. These labels are manually reviewed before being uploaded centrally, updating the thesauri lists for all users automatically. This ensures that the data remains consistent and interoperable with other datasets, while still allowing flexibility for unique requirements.

The system also supports data migration through the 'Data Import' module. New records can be entered using the ‘Data Input’ module. Additionally, data entries can be queried, filtered, modified, and exported into various file formats (the HTML-format is recommended) through the 'Data Explorer' module. An interactive map is also provided for easy management of site locations.

Please note that this is an early public release, and further improvements are recommended. For example, the data import functionality is still to be refined, and integration with a data repository would further enhance the system's capabilities.

Directory Structure

├── database
│   ├── data                 # postgresql database bind mount
│   └── ERD
│
├── frontend
│   ├── bootstrap-scss
│   ├── css
│   ├── img
│   ├── js
│   ├── sass
│   │   └── scss files       # are compiled to css files
│   ├── html files
│   └── Dockerfile
│
├── web-api
│   ├── build/libs
│   │   └── web-api.jar
│   ├── src/main
│   │   ├── java/arbodat/plus
│   │   │   ├── controller
│   │   │   ├── model
│   │   │   ├── repository
│   │   │   └── service
│   │   │       ├── migration_mapper
│   │   │       └── MigrationService
│   │   └── resources
│   │       └── application.properties
│   ├── build.gradle
│   └── Dockerfile
|
├── node-proxy
│   ├── server.js
│   ├── package.json
│   └── Dockerfile
│
├── info
│   ├── DANTE-terminologies
│   ├── API-URLs
│   └── data-migration-table-mapping
:
├── .env
├── .gitignore
└── docker-compose.yml

Start ArboDat+ Application:

Requirements: Docker

docker compose --profile prod up -d --build

Next, open a web browser and go to http://localhost

Export ArboDat+

• Build Docker Images:
  docker compose --profile prod build --no-cache
• Export and bundle Docker Images:
  docker save -o ArboDat+.tar postgres:16 arbodat_plus-frontend:latest arbodat_plus-web-api:latest arbodat_plus-node-proxy:latest
• Load Docker Images:
  docker load -i ArboDat+.tar
• Start ArboDat+ via Docker:
  docker compose up

Development

Start ArboDat+ via Docker in dev mode:
docker compose --profile dev build --no-cache
docker compose --profile dev up --build

• bind mount of frontend folder into nginx container
  (auto update of frontend changes while Application is running)
• node-proxy is available at http://localhost:3000

Database - PostgreSQL

Database is created using postgres:16 Docker Image

• Creation of test database:
  docker run --name test-database -p 5432:5432 --env POSTGRES_PASSWORD=password -d postgres:16

Web API - Spring Boot

Web API (backend) is built with Spring Boot 3.3, using Gradle 8.8 as the build tool and JDK 17 as the runtime environment.

• Run Web-API:
  Gradle -> Tasks -> application -> bootRun

• Build web-api.jar:

  • Windows:
    cd web-api && gradlew build && cd ..

  • Linux/macOS:
    cd web-api && chmod u+x gradlew && cd .. (make gradlew file executable)
    cd web-api && sudo ./gradlew build && cd ..

Frontend

• Compile css files from scss files via Sass
  • Recommended settings for Live Sass Compiler:
    copy this to .vscode/settings.json:

    "liveSassCompile.settings.formats": [
        {
            "format": "compressed",
            "extensionName": ".min.css",
            "savePath": "/frontend/css"
        }
    ],
    "liveSassCompile.settings.forceBaseDirectory": "/frontend/sass"
    

  • Live Sass Compiler -> Watch Sass (to generate css files)

License

See LICENSE.md and THIRD_PARTY_LICENSES.md for details