FinBIF2GBIF Bridge

FinBIF2GBIF is a software bridge between the Finnish Biodiversity Information Facility (FinBIF) and the Global Biodiversity Information Facility (GBIF) data registry.

This repository contains an R language based OpenShift deployment template (see section "Deploy") to launch a container based HTTP API that serves Darwin Core Archives of FinBIF collections. The same container is periodically deployed as a cronjob that syncronises the archives with the FinBIF data warehouse; and the collection metadata with the GBIF registry.

The data syncronisation configuration is controlled by the file, config.yml (see section "Configure").

Deploy

Local

Either build directly from the Dockerfile or use a prebuilt image from the GitHub container registry.

docker pull ghcr.io/luomus/finbif2gbif:latest

A docker-compose file is also included in this repository for local deployment (see also section "Testing").

OpenShift

Use the following to deploy to an OpenShift instance.

./oc-process.sh -f template.yml -e .env  | oc create -f -

Note the empty required parameters in the template file to infer the variables needed in a .env file (not provided).

Configure

The file config.yaml is used to configure the syncronisation of Darwin Core Archives and GBIF metadata with the FinBIF data warehouse. The example below enables all collections and will share title, description, language and license metadata with the GBIF data registry. It also specifies the default set of fields to include in all Darwin Core Archives and sets the maximum number of rows per occurrence record text file inside the archive files. For the collection HR.447 the records have been filter so that only records from the year 2015 onwards are included.

default:
  enabled: true
  metadata:
    title: long_name
    description: description
    license: intellectual_rights
  fields:
  - occurrenceID
  - basisOfRecord
  - eventDate
  - country
  - footprintWKT
  - geodeticDatum
  - coordinateUncertaintyInMeters
  - kingdom
  - scientificName
  - taxonRank
  nmax: 2.5e4
  filters:

HR.447:
  filters:
    date_range_ymd: ["2015-01-01", ""]

Testing

A second docker-compose file is included for running unit tests. It is run on each push to this repository via GitHub actions.

docker-compose --file docker-compose.test.yml build
docker-compose --file docker-compose.test.yml run -u $(id -u) su