cog-uk.js

Create an API client

const coguk = require("cog-uk.js");
const username = "test-username";
const token = "973db08f-8d68-4434-96cd-068d66d1dfa4";
const client = coguk(username, token);

Authenticate credentials

const ok = await client.authenticate();
if (ok) {
  // Valid credentials
}
else {
  // Invalid credentials
}

Submit Biosample

const sample = {
  "adm1": "UK-ENG",
  "central_sample_id": "BIRM-XXXXX",
  "collection_date": "2020-03-22",
  "source_age": 29,
  "source_sex": "M",
  "secondary_accession": "EPI_ISL_XXXXXX",
  "secondary_identifier": "hCov-19/England/Patient0/2020",
  "adm2": "WEST MIDLANDS",
  "collecting_org": "Queen Elizabeth Hospital Birmingham",
  "root_sample_id": "H20XXXXXXXX",
  "sample_type_collected": "swab",
  "sender_sample_id": "QELAB-01",
  "swab_site": "nose",
  // See https://docs.covid19.climb.ac.uk/majora/add_sample#reference for full list of biosample fields
  
  "library_name": "BIRM-LIBRARY-20200322",
  // See https://docs.covid19.climb.ac.uk/majora/add_library#reference for full list of library fields

  "run_name": "BIRM-my_first_run",
  // See https://docs.covid19.climb.ac.uk/majora/add_sequencing#reference for full list of sequencing fields
};
const results = await client.submit(validSample);

results:

{
  "success": true,
  "status": "updated",
  "detailedMessages": {},
  "messages": {},
  "error": null
}

Submit an invalid Biosample

const sample = {
  "adm1": "England",
};
const results = await client.submit(validSample);

results:

{
  "success": false,
  "status": "ignored",
  "detailedMessages": {
    "central_sample_id": [
      {
        "message": "This field is required.",
        "code": "required",
        "source": "biosample"
      }
    ],
    "adm1": [
      {
        "message": "Select a valid choice. England is not one of the available choices.",
        "code": "invalid_choice",
        "source": "biosample"
      }
    ],
    "received_date": [
      {
        "message": "You must provide a received date for samples without a collection date",
        "code": "",
        "source": "biosample"
      }
    ]
  },
  "messages": {
    "central_sample_id": "This field is required.",
    "adm1": "Select a valid choice. England is not one of the available choices.",
    "received_date": "You must provide a received date for samples without a collection date"
  },
  "error": "Errors in the following fields: central_sample_id, adm1, received_date"
}