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Taxonomic Infrastructure

Table of Contents

Build Status

This is the NSL (National Species List) Services Application developed at the Australian National Botanic Gardens in association with CHAH, the ALA and the IBIS team.

Services

The NSL services provide a relatively generic set of services for searching Names, References and Authors as well as accessing classification trees of taxons.

The NSL is (and probably always will be) a work in progress, we’ll be adding a roadmap and more doco here as we go.

This code is Licensed under the Apache 2 License and we welcome contributions from the taxonomic community.

Please use Github issues for any bug reports.

Shard ID ranges

For Australian NSL infrastructure we are splitting the ID ranges used across different known shards. This is not essential but it does mean we have a means to discriminate data sources on IDs if somehow we manage to loose track.

The current allocated ranges are:

  • Vascular (APNI) 1000 - 10,000,000 + 50,000,001 - 60,000,000

  • Moss 10,000,001 - 20,000,000

  • Algae 20,000,001 - 30,000,000

  • Lichen 30,000,001 - 40,000,000

  • DAWR 40,000,001 - 50,000,000 (Aust. Dept. of Agriculture and Water Resources)

  • Fungi 60,000,001 - 70,000,000

  • AFD 70,000,001 - 80,000,000

There is a confluence page for the NSL infrastructure as well at https://www.anbg.gov.au/ibis25/pages/viewpage.action?spaceKey=NSL&title=NSL+Project+2.0

Building and Running

This is a standard Grails 5 project. You can use all the standard grails tasks to build and run this project. You will need some supporting services i.e.

  1. A mapper

  2. postgresql database with the NSL schema loaded

  3. LDAP with users

Tip
 See Developing with supporting services below for how to get these running for development using the included docker-compose scripts.

There are two dependencies you need to build and install in your local maven before running services, grails-shiro and nsl-domain-plugin.

  1. git clone git@github.com:bio-org-au/grails-shiro.git ; cd grails-shiro ; ./gradlew publishToMavenLocal

  2. git clone git@github.com:bio-org-au/nsl-domain-plugin-g3.git ; cd nsl-domain-plugin-g3 ; ./gradlew publishToMavenLocal

To run the services in development mode just run grails run-app which will run up the service in it’s own tomcat instance locally. You can also use the gradle task bootRun e.g. ./gradlew bootRun.

To create a runnable war, or a war that can be installed in Tomcat run ./gradlew bootWar

The services work nicely within IntelliJ IDEA just import the project.

Building and deploying docker image.

To build a war file you can use grails war or you can use ./gradlew assemble. This will build a war file and put it in the build/libs directory.

To publish to docker use the gradle task ./gradlew dockerPublish. Note you will have to be logged into docker hub to publish.

Warning
 Note we’re currently publishing to biodiversity/ on docker hub. Change the dockerRepo property in the gradle.properties file to your own repository.
Note
 The docker image runs the services as the nsl_user UID: 5000 GID: 5000 in the container. This user will be mapped to the host user:group with those IDs. It may be useful to assign a user to that ID in the host, but not essential.

Developing with supporting services

We have supplied a docker-compose driven script to run up a mapper and ldap server. Follow thes steps to get it running:

  1. Install docker, use the docs/docker.adoc document as a guide.

  2. Make sure the environment variables in the bin/devel-up.sh script are correct, mainly that the postgresql port is correct.

  3. The script will alter your database to make the mapper tables point at "biodiversity.local", So you’ll need to add the following lines to /etc/hosts before you run it:

    127.0.0.1 biodiversity.local
127.0.0.1 id.biodiversity.local

  4. run the script `bin/devel-up.sh

The script uses docker-compose up to run the mapper and ldap. The LDAP is at port 10389 and the mapper is on port 7070.

Warning
 This exposes the ports on the host machine, so the services won’t work if you run them via the included Dockerfile, as that runs within another docker container and doesn’t have a network connection/route to the exposed ports.

By default the grails run-app or ./gradlew bootRun will try and use the config file at "${projectDir.absolutePath}/etc/nsl/services-config-g3.groovy" (see build.gradle task bootRun). This expects the

Tip
 The LDAP server include has a user called test with the password test so you can log into the editor and the services

Stopping the docker containers

to stop the mapper and ldap run bin/devel-down.sh.