ckanext-gbif 2.0.0

A CKAN extension that that connects with the GBIF API.

ckanext-gbif

A CKAN extension that that connects with the GBIF API.

Overview

This extension retrieves additional data (e.g. DQIs) from the GBIF API for a record with an associated GBIF ID.

This extension also provides some templates for displaying these data.

Installation

Path variables used below:

• $INSTALL_FOLDER (i.e. where CKAN is installed), e.g. /usr/lib/ckan/default
• $CONFIG_FILE, e.g. /etc/ckan/default/development.ini

1. Clone the repository into the src folder:

cd $INSTALL_FOLDER/src
git clone https://github.com/NaturalHistoryMuseum/ckanext-gbif.git

2. Activate the virtual env:

. $INSTALL_FOLDER/bin/activate

3. Install the requirements from requirements.txt:

cd $INSTALL_FOLDER/src/ckanext-gbif
pip install -r requirements.txt

4. Run setup.py:

cd $INSTALL_FOLDER/src/ckanext-gbif
python setup.py develop

5. Add 'gbif' to the list of plugins in your $CONFIG_FILE:

ckan.plugins = ... gbif

Configuration

There are a couple of options to be specified in your .ini config file.

Template variables [REQUIRED]

Name	Description
ckanext.gbif.organisation_key	For linking to the dataset publisher (i.e. https://gbif.org/publisher/ORG_KEY)
ckanext.gbif.dataset_key	For linking to the dataset itself (i.e. https://gbif.org/dataset/DATA_KEY)

Usage

Actions

gbif_record_show

Get the associated GBIF data for a record.

from ckan.plugins import toolkit

gbif_record = toolkit.get_action(u'gbif_record_show')(context, {
    u'occurrence_id': record_gbif_occurrence_id
    })

Templates

The templates inherit from record/specimen.html and record/dwc.html and will insert a link to the GBIF view in the content_primary_nav block.

Testing

Test coverage is currently extremely limited.

To run the tests in this extension, there is a Docker compose configuration available in this repository to make it easy.

To run the tests against ckan 2.9.x on Python3:

1. Build the required images

docker-compose build

2. Then run the tests. The root of the repository is mounted into the ckan container as a volume by the Docker compose configuration, so you should only need to rebuild the ckan image if you change the extension's dependencies.

docker-compose run ckan

The ckan image uses the Dockerfile in the docker/ folder which is based on openknowledge/ckan-dev:2.9.