EJP-RD-Beacon-in-a-Box

This repository is a modified version of the Beacon2 Reference Implementation (B2RI) and contains a stand-alone Beacon instance designed to allow for the sharing of metadata of datasets.

This repo contains:

• The (Python 3.7+) source code for beacon,

Local installation instructions(Docker)

Instructions

Local installation instructions(Dockerless)

Instructions

Importing metadata into the Beacon-in-a-box

To import metadata into your Beacon instance please use the Beacon-import-tools.

Query Endpoints

Individuals endpoint

Method : GET

http GET http://localhost:5050/api/individuals/

Querying this endpoit it should return all the variants of the beacon (paginated):

Method : POST

http POST http://localhost:5050/api/individuals/ --json < request.json

You can use POST to make the previous query. With a request.json file like this one:

{
    "meta": {
        "apiVersion": "2.0"
    },
    "query": {
        "filters": [
                {
                "id": "HP_0001252"
                }
        ],
        "includeResultsetResponses": "HIT",
        "pagination": {
            "skip": 0,
            "limit": 10
        },
        "testMode": false,
        "requestedGranularity": "record"
    }
}

Above request will return all the individuals with "HP_0001252" phenotype.

You can execute:

But you can also use complex filters:

{
    "meta": {
        "apiVersion": "2.0"
    },
    "query": {
        "filters": [
            {
                "id": "obo:NCIT_C28421",
                "value": "obo:NCIT_C16576"
            }
        ],
        "includeResultsetResponses": "HIT",
        "pagination": {
            "skip": 0,
            "limit": 10
        },
        "testMode": false,
        "requestedGranularity": "record"
    }
}

Catalogs endpoint

Method : GET

http GET http://localhost:5050/api/catalogs/ --json < request.json

Above request return all records.

Method : POST

http POST http://localhost:5050/api/catalogs/ --json < request.json

Query Request Body:

{ 
"$schema": "https://json-schema.org/draft/2020-12/schema",
 "meta":{},
 "query": {
      "filters": [
        {
          "id": "description",
          "value": "%genome comparison%",
        },
        {
          "id": "resourceTypes",
          "value": " BiobankDataset"

        }
      ]
    }
}

RESPONSE

{
  "meta": {},

  "responseSummary": 
  {
    "exists": true,
    "numTotalResults": 1
  },
  "response": {
    "resultSets": [
      {
        "resultsCount": 1,
        "results": [
          {
          "createDateTime": "2017-04-30T00:00:00+00:00",
          "description": "The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. ",
          "externalUrl": "https://www.nature.com/articles/sdata201625, https://jimb.stanford.edu/giab-resources",
          "id": "EGAD00001008097",
          "name": "The Genome in a Bottle Consortium (GIAB)",
          "updateDateTime": "2017-04-30T00:00:00+00:00",
          "resourceTypes": ["BiobankDataset"],
          "organisation": ["UOL"]

          }
        ],
        "resultsHandover": null
      }
    ]
  },
  "beaconHandovers": []
  }