Species lists and traits

This is a grails application for managing species lists. It supports:

• Upload of species profile data in CSV format
• UI for viewing and faceting species
• Supports any number of key/value pairs
• JSON services used by
  • BIE - species pages (https://bie.ala.org.au)
  • Biocache - indexing occurrences (https://biocache.ala.org.au)
• Supports single owner & multiple editors of a single list
• Lists can be tagged as:
  • authoritative
  • conservation
  • sensitive
• Supports sensitive species lists

Architecture

• Grails web application
• MySQL database

Installation

There is an Ansible playbook for this application here ala-install/ansible/species-list-standalone.yml See example inventory ala-install/ansible/inventories/vagrant/species-list-vagrant

Setting up for development

This application only needs a running MySQL instance and the app itself. There is a docker compose file that can be used to run a local MySQL instance. To use, install docker and docker compose and run:

docker-compose -f mysql.yml up

This should setup a running MySQL instance and expose port 3306. This is for development purposes only. Once the docker instance is running, the app can be started using

grails run-app

Changelog

• **Version 5.2.1 **:
  • improved the performance of rematching processing
  • Fixed list csv downloads has duplicate columns
  • Fixed the broken species list upload from spatial issue
  • Replaced deprecated functions provided by AuthService plugin
  • Grails 6 upgraded
• Version 3.0:
  • Grails 3, Lucene 5 or above
• Version 2.0:
  • upgraded to Grails 3
• Version 1.0:
  • upgraded to asset pipeline and grails 2.5.6
  • fixed unit and integration tests

Release

• Version 5.2.1: Database change:

  • rematch_Log table changed:

  DROP TABLE IF EXISTS `rematch_log`;
  
  CREATE TABLE `rematch_log` (
  `id` bigint NOT NULL AUTO_INCREMENT,
  `version` bigint NOT NULL,
  `end_time` datetime(6) DEFAULT NULL,
  `processing` varchar(255) NOT NULL,
  `start_time` datetime(6) NOT NULL,
  `by_whom` varchar(255) NOT NULL,
  `status` varchar(255) DEFAULT NULL,
  `latest_processing_time` datetime(6) NOT NULL,
  `history` longtext,
  PRIMARY KEY (`id`)
  ) ENGINE=InnoDB AUTO_INCREMENT=1 DEFAULT CHARSET=utf8mb4;
  

After the database change, change 'dataSource.dbCreate=none' into local config file to speed up the application startup.