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Beacon 4 Images

This repository is an implementation of the beacon for images model:

  • The (Python 3.9+) source code for beacon,
  • A MongoDB database with sample data to demo the capabilities of the Beacon API images.

Deployment steps

Switch to deploy folder:

cd deploy

Build the containers:

docker-compose up -d --build

Go to http://localhost:5054/api and your API will be running there.

Inject data

From deploy folder, switch to data folder:

cd data

Copy data to mongo container:

docker cp datasets.json deploy-db-images-1:tmp/datasets.json
docker cp measurements.json deploy-db-images-1:tmp/measurements.json
docker cp features.json deploy-db-images-1:tmp/features.json
docker cp conditions.json deploy-db-images-1:tmp/conditions.json
docker cp occurrences.json deploy-db-images-1:tmp/occurrences.json

Inject data to mongoDB:

docker exec deploy-db-images-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27019/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets
docker exec deploy-db-images-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27019/beacon?authSource=admin" --file /tmp/measurements.json --collection measurements
docker exec deploy-db-images-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27019/beacon?authSource=admin" --file /tmp/features.json --collection features
docker exec deploy-db-images-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27019/beacon?authSource=admin" --file /tmp/conditions.json --collection conditions
docker exec deploy-db-images-1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27019/beacon?authSource=admin" --file /tmp/occurrences.json --collection occurrences

*Individuals can also be filled in.

Extract filtering terms:

docker exec beacon-images python beacon/db/extract_filtering_terms.py

Make queries:

curl \
  -H 'Content-Type: application/json' \
  -X POST \
  -d '{
    "meta": {
        "apiVersion": "2.0"
    },
    "query": {
        "requestParameters": {        },
        "filters": [
{"id": "312437"}],
        "includeResultsetResponses": "HIT",
        "pagination": {
            "skip": 0,
            "limit": 100
        },
        "testMode": false,
        "requestedGranularity": "record"
    }
}' \
  http://localhost:5054/api/conditions