elixir-europe / plant-brapi-etl-faidare

Harvest and index meta data from BrAPI endpoints for data access through the plant-faidare data lookup portal (https://github.com/elixir-europe/plant-faidare).

Elixir plant Breeding API JSON ETL

• Extract BrAPI endpoint.
• Transform extracted data (into Elasticsearch bulk json, into JSON-LD, into RDF)
• Load JSON into Elasticsearch or RDF into a virtuoso

I. Execution

From source code

Requirements:

• Python version 3.6+
• Python dependencies (pip install -r requirements.txt)
• OR (prepeferd) use a virtual environment (pipenv, virtualenv, conda, etc) : pipenv install

The `main.py` script can be used to launch the full BrAPI to elasticsearch or BrAPI to virtuoso ETL. To get the usage help run the following command:

```sh
$ pipenv run python main.py --help

OR (if you have installed the dependencies in your environment)

$ python3 main.py

II. Configuration

ETL process configurations

The configurations for the ETL process is defined in the ./config folder.

Data sources

The BrAPI data source are described in the ./sources folder in JSON-LD format using the schema.org vocabulary. You can add data sources in this folder using one of the other data source as an example.

Here is an example of data source description:

{
  "@context": {
    "schema": "http://schema.org/",
    "brapi": "https://brapi.org/rdf/"
  },
  "@type": "schema:DataCatalog",
  "@id": "http://pippa.psb.ugent.be",
  "schema:identifier": "VIB",
  "schema:name": "VIB PIPPA",
  "brapi:endpointUrl": "https://pippa.psb.ugent.be/pippa_experiments/brapi/v1/"
} 

The @id field contains the URI identifying the data source (we use the URL of the official web site for convinience), the schema:identifier contains a short identifier for this data source, the schema:name contains the display name and brapi:endpoint contains the URL of the BrAPI endpoint.

BrAPI endpoints requirements

Current BrAPI version: 1.3. Backward compatibility with 1.2 is ensured to a certain extent.

The BrAPI endpoint must implement the required calls (also listed in ./config/entities/ json files, note that the first element of each "call" array is the recomended implementation): Mandatory:

• /brapi/v1/calls GET
• /brapi/v1/studies GET
• /brapi/v1/studies/{studyDbId}

Recommended:

• /brapi/v1/germplasm GET
• /brapi/v1/germplasm/{germplasmDbId} GET
• /brapi/v1/variables GET
• /brapi/v1/locations GET
• /brapi/v1/locations/{locationDbId} GET
• /brapi/v1/studies/{studyDbId}/germplasm GET
• /brapi/v1/studies/{studyDbId}/observationvariables GET
• /brapi/v1/trials GET
• /brapi/v1/trials/{trialDbId} GET

Optional:

• /brapi/v1/germplasm/{germplasmDbId}/attributes GET
• /brapi/v1/germplasm/{germplasmDbId}/pedigree GET
• /brapi/v1/programs GET

Experimental:

• /brapi/v1/observationunits GET (backward compatibility with phenotype-search)
• /brapi/v1/studies/{studyDbId}/observationunits GET

See README-extract-transform-for-FAIDARE.md for specific details on BrAPI to elasticsearch ETL.