Project Structure

The project is divided into two apps:

1. A React powered frontend, created using Create React App
2. A backend, powered by AdonisJs and a MySQL database, exposing a REST API

Setup instructions

Follow these instructions to get the project up and running:

1. Install Node.js.

Make sure you have Node >= v8.10 installed on your machine.

2. Install Yarn.

Make sure you have Yarn v1 installed on your machine.

3. Install dependencies.

   This will install the Node dependencies for both projects at once.

   cd jembi-fhir-server/
   yarn

4. Run migrations

   yarn workspace backend node ace migration:run

5. Start the two apps

   yarn workspace backend
   
   cd backend/
   yarn workspace frontend

You only need to start the backend application for this demo

6. And, you're all set up!

Working on the app

Running tests

yarn workspace backend test test/ObservationsEndpoint.ts

Running lint fix

yarn lint

yarn lint:fix

Creating a resource

curl -L -X POST "http://127.0.0.1:<port>/v1/Observations" \
-H "Content-Type: application/json" \
--data-raw '{ "resourceType" : "Observation", ... }'

Alternatively, you should use an API testing tool like Postman for convenience

NB: Remember to use adapted request body sample in the Assumptions about app section.

Querying a resource

curl -L -X GET "http://127.0.0.1:<port>/v1/Observations?category=vital-signs&code=LOINC"

Where LOINC is a string value for the code

NB: Multi code search i.e ...&code=[LOINC{,LOINC2...}] is not implemented

curl -L -X GET "http://127.0.0.1:<port>/v1/Observations?category=vital-signs&date=[date]"

curl -L -X GET "http://127.0.0.1:<port>/v1/Observations?category=vital-signs&date=[date]{&date=[date]}"

The query parameter and value ?category=vital-signs should be added otherwise an error will returned.

The database needs to populated with sufficient data for running queries against the API.

Assumptions about the app

1. The structure of the POST request body resembles the Observation resource here

Here's the adapted structure of the request body

{
  "resourceType" : "Observation",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: See jembi-fhir-server/backend/app/Models/DomainResource
  "identifier" : [{ Identifier }], // Business Identifier for observation
  "status" : "<code>", // R!  registered | preliminary | final | amended +
  "code": { CodeableConcept }, // R!  Type of observation (code / type)
  "effectivePeriod" : { Period },
  "issued" : "<instant>", // Date/Time this version was made available
  "valueQuantity": { Quantity },
  "interpretation": [
    { 
      "low" : { Quantity(SimpleQuantity) }, // C? Low Range, if relevant
      "high" : { Quantity(SimpleQuantity) }, // C? High Range, if relevant
      ...
      "text" : "<string>" // Text based reference range in an observation
    }
  ]
}

Here's a sample of the adapted request body

{
  "identifier": [
    {
      "use": "official",
      "system": "http://www.bmc.nl/zorgportal/identifiers/observations",
      "value": "6325"
    }
  ],
  "status": "final",
  "code": {
    "text": "Negative for Chlamydia Trachomatis rRNA",
    "coding": [
      {
        "system": "http://loinc.org",
        "symbol": "11557-6",
        "display": "Carbon dioxide in blood"
      }
    ]
  },
  "effectivePeriod": {
    "start": "2013-04-02T10:30:10+01:00",
    "end": "2013-04-05T10:30:10+01:00"
  },
  "issued": "2013-04-03T15:30:10+01:00",
  "valueQuantity": {
    "value": 6.2,
    "unit": "kPa",
    "system": "http://unitsofmeasure.org",
    "code": "kPa"
  },
  "interpretation": [
    {
      "coding": [
        {
          "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation",
          "code": "H",
          "display": "High"
        }
      ]
    }
  ],
  "referenceRange": [
    {
      "text": "Text based reference range in an observation",
      "low": {
        "value": 4.8,
        "unit": "kPa",
        "system": "http://unitsofmeasure.org",
        "code": "kPa"
      },
      "high": {
        "value": 6.0,
        "unit": "kPa",
        "system": "http://unitsofmeasure.org",
        "code": "kPa"
      }
    }
  ]
}

2. Data to the POST endpoint has beeen validated on frontend and can be reasonably realied on.

3. Several attributes were ommited from the Observation model under jembi-fhir-server/backend/app/Models/Observation to make scope manageable.

4. Observation and DomainResource have a hasOne relationship. An Observation has one DomainResource associated with it at the time of its creation and that this DomainResource houses the logical ID and meta information which is populated by default.

5. Resource and DomainResource have been merged into one representation to make scope manageable. You'll find some attributes from Resource such as id referenced in DomainResource.

6. In the interest of time, the exercise didn't focus developing extensive unit tests and generating seed values for extensive testing.

7. The response has been standardised under jembi-fhir-server/backend/contracts/interfaces/ObservationsInterface

8. ReferenceRange accepts a single instance of even though it has a hasMany relationship with the parant model Observation. The first object will be read from the array passed to it only.