ckanext-fair3r

The CKAN plugin behind fair3r.fr, a catalogue of research datasets (animal models, phenotyping). It adds the FDF (FAIR3R Dataset Form): a dynamic, ontology-driven metadata form built from a JSON schema. It turns those metadata into DataCite, DCAT-AP, Croissant and schema.org, and gives the site its theme and a few features around datasets.

For a ready-to-run FAIR3R stack with this plugin already wired up, see fair3r-docker-alt. The rest of this page is for adding the plugin to your own CKAN 2.12.

Features

• FDF form: dataset creation and editing with a form generated from fdf_schema.json, which looks terms up in external databases (ORCID, ROR, ontologies, genes, alleles, strains) and is checked again on the server. The answers are stored on the dataset (fdf_output_json) with DataCite-shaped datacite.* extras derived from them.
• Completeness score on the dataset page and live in the form.
• Metadata for other systems: DataCite DOI metadata through ckanext-doi, DCAT-AP, Croissant and schema.org through ckanext-dcat, a sitemap.
• Publishing and downloading: a "Publish" button (private -> public, one way), "Download all" as one ZIP, a fix for a CKAN/xloader race that can turn a just-published dataset back to draft.
• Resource form: several files at once with progress, duplicate-name warning, routing of large files to Zenodo with ckanext-zenodo.
• Accounts and access: account request form, members-only organization/group activity streams, HTML emails.
• Theme of fair3r.fr, French translations.

The full specification is in docs/: architecture, the FDF schema, every workflow step by step, metadata mapping, security, configuration and operations.

Requirements

• CKAN 2.12, with Redis and the background worker (ckan jobs worker) running: they're used to fix the draft race and to limit account requests.

• ckanext-doi, FAIR3R's fork, published on PyPI as ckanext-fair3r-doi (the ckanext-doi package on PyPI is a different one, the original). It must be installed, since this plugin uses its interface. Enabling it (and having a DataCite account) is only needed to mint DOIs.

• Optional, each one adds something when enabled:

  Plugin	Adds
  dcat, structured_data, croissant (ckanext-dcat)	The FAIR3R RDF profiles
  activity (CKAN core)	Members-only activity streams
  pages (ckanext-pages, PyPI: ckanext-fair3r-pages)	Pages and Blog links in this plugin's header
  citations (ckanext-citations)	The "FAIR & Impact" panel, with the completeness score
  zenodo (ckanext-zenodo)	Large files on Zenodo, with a DOI
  contact (ckanext-contact)	The contact page; its ckanext.contact.mail_to is where account requests go

Installation

1. In CKAN's virtualenv:

   pip install ckanext-fair3r ckanext-fair3r-doi
   

2. Enable the plugin in ckan.ini. The first-listed plugin's templates win, and this plugin's header replaces CKAN's: keep pages before fair3r, or the Pages and Blog links disappear.

   ckan.plugins = ... dcat structured_data croissant pages fair3r doi citations ...
   

3. Optional, for the FAIR3R RDF output (with ckanext-dcat):

   ckanext.dcat.rdf.profiles = fair3r_dcat_ap
   ckanext.dcat.croissant.profiles = fair3r_croissant
   ckanext.dcat.structured_data.profiles = fair3r_schemaorg
   

4. Fetch the FDF schema, then keep it up to date daily, as the CKAN user (cron). The package doesn't include it: until the first update-schema, the FDF form is empty.

   ckan -c /path/to/ckan.ini fair3r update-schema
   

   0 0 * * * /path/to/venv/bin/ckan -c /path/to/ckan.ini fair3r update-schema
   

   The CKAN user needs write access to the package's ckanext/fair3r/schema/ directory.

5. Restart CKAN and its worker.

Configuration

More in docs/operations.md, with troubleshooting.

Commands

Development

git clone https://github.com/Phen-ICS/ckanext-fair3r.git
cd ckanext-fair3r
pip install -e .
pip install -r dev-requirements.txt

Code style, checked in CI (ruff 0.16.0):

ruff format ckanext
ruff check ckanext --fix

Tests

docker exec -u ckan -it ckan-app pytest --ckan-ini=/plugins/ckanext-fair3r/test.ini /plugins/ckanext-fair3r/ckanext/fair3r/tests

Always pass --ckan-ini: the test fixtures empty the database they run against, and refuse to run unless its name contains test. The test.ini at the repository root is for the DEV container; ckanext/fair3r/tests/test.ini, shipped in the package, is the one the integration server uses - keep their plugin lists in sync.

Translations

English source strings, French catalogue in ckanext/fair3r/i18n/fr/: see docs/operations.md for the extract / update / compile steps.

License

Released under the GNU Affero General Public License (AGPL) v3.0. See the file LICENSE for details.