Skip to content

Latest commit

 

History

History
439 lines (352 loc) · 13.5 KB

README.md

File metadata and controls

439 lines (352 loc) · 13.5 KB
Raw

clods

Scc Count Badge Scc Cocomo Badge Clojars Project

A library, a web service and set of tools for UK health and care organisational data.

Health and Social Care Organisation Reference Data is published by NHS Digital under standard DCB0090.

clods is designed to provide "location" services down to the granularity of an organisational site using this reference data.

clods part of a suite of supporting foundational data and computing services that help to answer questions about the 'who', 'what', 'when', 'how' and 'why' of health and care data.

This software provides both a library and web service. As a library, it can easily be embedded into a larger application. As a microservice, it can easily be embedded into a suite of foundational platform services. It provides both a plain REST API as well as a HL7 FHIR API (r4).

You can obtain general practitioner information for a specific GP surgery using ods-weekly.

More finely-grained location services (e.g. ward, bed) are provided by other modules as part of a unified concierge location service. Ward and bed location and status data are usually provided as part of a patient administrative system rather than reference data services, but this aims to provide a seamless application programming interface (API) in order to appropriately record the context of the capture of any clinical data.

Design goals

At its core, the software provides a close representation of the original source data while also providing a more abstract set of systems that will be federatable; that means application software working across international boundaries with runtime harmonisation and abstractions across multiple backend services.

  • Data-first - structured, self-describing data.
  • Properties as first-class abstractions rather than rigid class based hierarchies.
  • Subject / predicate / object (entity / attribute / value) triples à la RDF.
  • Standards-based - providing foundational software and data services.
  • An 'open-world' assumption
  • Client-driven graph-like queries.

Public sector data should be open, published and self-describing, with mechanisms to permit computability. That means we can write software that automatically updates against master indexes of a range of important public sector data.

When running as either a library or microservice, the only dependency is a filesystem.

In the olden days, we cared for individuals servers and gave them names, analogous to looking after pets. They'd be long-lived and we'd run services on them. You'd have administrators manually logging in to update-in-place, upgrading either the version of the software or updating the backing data.

You can still use this model for this and the other PatientCare software but the more modern approach is to treat your computing and data infrastructure as cattle. Unlike a pet, you don't usually name your cattle, and you might have a significant turnover in those cattle. As such it is entirely reasonable to spin up new versions of this service with new updated data.

As such, this, and the other PatientCare services are designed to automate as many steps as possible.

Getting started:

You'll need to install clojure for the best experience but it is possible to run using a pre-built jar. See below for information about the jar files.

Importing data

This service needs a directory on a filesystem to operate.

The NHS organisational data includes information about NHS organisations. To enable geographical services, clods combines these data with NHS geographical data using the 'NHS postcode directory'. You can use nhspd as a standalone service, but for convenience, clods includes that tooling.

1. Choose the location of your index files.

In these examples, we'll use

  • /var/local/ods-2021-02 for our organisation index
  • /var/local/nhspd-2020-11 for our postcode index

You can choose to use a single directory and update-in-place, or build a new repository at intervals. I prefer read-only, immutable backing data by default, so favour the latter.

We also need to specify a temporary cache for downloaded data.

For these examples, we'll use

  • /var/tmp/trud

2. Initialise the postcode service

You may already have nhspd running; use the index you use for that.

If not, let's get one set-up

$ clj -M:nhspd /var/local/nhspd-2020-11

After a few minutes, the NHS postcode directory index will have been downloaded and imported.

3. Initialise the organisation service

You will need a NHS Digital TRUD API key.

Login to the NHS Digital TRUD and find your API key under your profile. Write that key to a file and link to it from the command-line:

$ clj -M:install --nhspd /var/local/nhspd-2020-11 --api-key /path/to/api-key.txt --cache-dir /var/tmp/trud /var/local/ods-2021-02

clods will proceed to download the latest distribution files from TRUD, or use the existing downloaded version in your local cache if available, and create an organisation index.

While you could embed all of this into a single Docker image for deployment, it might be better to instead link to a shared read-only filesystem and simply link to the latest backend data.

Running a simple REST server

To run as a microservice, you need to include the paths of the both an ODS index, and an NHSPD index as well as the port to run on.

$ clj -M:serve /var/local/ods-2021-02  /var/local/nhspd-2020-11 8080

There are three endpoints:

Let's get NHS postcode data about a postcode:

$ curl -H "Accept: application/json" localhost:8080/ods/v1/postcode/CF144XW

Result:

{"CANNET":"N95","PCDS":"CF14 4XW","NHSER":"W92","SCN":"N95","PSED":"62UBFL16","CTRY":"W92000004","OA01":"W00009154","HRO":"W00","OLDHA":"QW2","RGN":"W99999999","OSWARD":"W05000864","LSOA01":"W01001770","OSNRTH1M":179319,"CANREG":"Y1101","OSHLTHAU":"7A4","CALNCV":"W99999999","OSGRDIND":"1","MSOA11":"W02000384","MSOA01":"W02000384","WARD98":"00PTMM","OLDHRO":"W00","CENED":"TNFL16","OLDPCT":"6A8","USERTYPE":"0","OSEAST1M":317551,"PCT":"7A4","PCD2":"CF14 4XW","NHSRLO":"W92","OSNRTH100M":1793,"DOTERM":"","STP":"W92","OSLAUA":"W06000015","OSHAPREV":"Q99","EDIND":"1","LSOA11":"W01001770","UR01IND":"5","CCG":"7A4","OSEAST100M":3175,"DOINTR":"199906","PCON":"W07000051","ODSLAUA":"052","OA11":"W00009154","OSCTY":"W99999999"}

Let's get ODS data about a known organisation:

$ curl -H "Accept: application/json" localhost:8080/ods/v1/organisation/7A4BV

Let's search for an organisation:

Simple search by name:

$ curl -H "Accept: application/json" 'localhost:8080/ods/v1/search?s=University%20Hospital%20Wales'

Let's search for GP surgeries within 1000m of a specific postcode.

$ curl -H "Accept: application/json" 'localhost:8080/ods/v1/search?roles=RO177&from-postcode=CF144XW&range=1000'

Result (here I pipe through jq to just give me the names):

$ curl -H "Accept: application/json" 'localhost:8080/ods/v1/search?roles=RO177&from-postcode=CF144XW&range=1000' | jq '.[] | .name'
"OUT OF HOURS SERVICE"
"WHITCHURCH ROAD SURGERY"
"CRWYS MEDICAL CENTRE"
"NORTH ROAD MEDICAL PRACTICE"

The results will be sorted by distance.

Each result is annotated with WGS84 latitude and longitude, to make it easier for onward geographical processing/plotting.

$ curl -H "Accept: application/json" 'localhost:8080/ods/v1/search?s=crwys&roles=RO177&from-postcode=CF144XW&range=1000' | jq              
[
  {
    "orgId": {
      "root": "2.16.840.1.113883.2.1.3.2.4.18.48",
      "assigningAuthorityName": "HSCIC",
      "extension": "W97041"
    },
    "contacts": [
      {
        "type": "tel",
        "value": "029 20524140"
      }
    ],
    "name": "CRWYS MEDICAL CENTRE",
    "operational": {
      "start": "1974-04-01",
      "end": null
    },
    "roles": [
      {
        "id": "RO72",
        "isPrimary": false,
        "active": true,
        "startDate": "2014-04-15",
        "endDate": null
      },
      {
        "id": "RO177",
        "isPrimary": true,
        "active": true,
        "startDate": "1974-04-01",
        "endDate": null
      }
    ],
    "orgRecordClass": "RC1",
    "active": true,
    "primaryRole": {
      "id": "RO177",
      "isPrimary": true,
      "active": true,
      "startDate": "1974-04-01",
      "endDate": null
    },
    "relationships": [
      {
        "id": "RE4",
        "startDate": "1999-04-01",
        "endDate": "2003-03-31",
        "active": false,
        "target": {
          "root": "2.16.840.1.113883.2.1.3.2.4.18.48",
          "assigningAuthorityName": "HSCIC",
          "extension": "4WK03"
        }
      },
      {
        "id": "RE4",
        "startDate": "2009-10-01",
        "endDate": null,
        "active": true,
        "target": {
          "root": "2.16.840.1.113883.2.1.3.2.4.18.48",
          "assigningAuthorityName": "HSCIC",
          "extension": "7A4"
        }
      },
      {
        "id": "RE4",
        "startDate": "2003-04-01",
        "endDate": "2009-09-30",
        "active": false,
        "target": {
          "root": "2.16.840.1.113883.2.1.3.2.4.18.48",
          "assigningAuthorityName": "HSCIC",
          "extension": "6A8"
        }
      }
    ],
    "location": {
      "address1": "THE CRWYS SURGERY",
      "address2": "WEDAL ROAD",
      "town": "CARDIFF",
      "county": "SOUTH GLAMORGAN",
      "postcode": "CF14 3QX",
      "country": "WALES",
      "uprn": "10008905579",
      "latlon": [
        52.714814004647714,
        -5.273869588498894
      ]
    },
    "isReference": false
  }
]

Running a FHIR-compatible server 🔥

$ clj -M:fhir-r4 /var/local/ods-2021-02 /var/local/nhspd-2020-11 8080

Let's try it:

$ curl -H "Accept: application/json" 'http://localhost:8080/fhir/Organization/2.16.840.1.113883.2.1.3.2.4.18.48|W93036'

Result:

{
  "resourceType": "Organization",
  "id": "W93036",
  "identifier": [
    {
      "use": "official",
      "system": "https://fhir.nhs.uk/Id/ods-organization",
      "value": "W93036"
    },
    {
      "use": "old",
      "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.18.48",
      "value": "W93036"
    }
  ],
  "active": true,
  "type": [
    {
      "coding": [
        {
          "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.17.507",
          "code": "RO72",
          "display": "OTHER PRESCRIBING COST CENTRE"
        }
      ]
    },
    {
      "coding": [
        {
          "system": "urn:oid:2.16.840.1.113883.2.1.3.2.4.17.507",
          "code": "RO177",
          "display": "PRESCRIBING COST CENTRE"
        },
        {
          "system": "http://hl7.org/fhir/ValueSet/organization-type",
          "code": "prov",
          "display": "Healthcare Provider"
        }
      ]
    }
  ],
  "name": "CASTLE GATE MEDICAL PRACTICE",
  "telecom": [
    {
      "system": "phone",
      "value": "01600 713811"
    }
  ],
  "address": [
    {
      "line": [
        "REAR OF MONNOW STREET"
      ],
      "city": "MONMOUTH",
      "district": "GWENT",
      "postalCode": "NP25 3EQ",
      "country": "WALES"
    }
  ],
  "partOf": {
    "type": "Organization",
    "identifier": {
      "use": "official",
      "system": "https://fhir.nhs.uk/Id/ods-organization",
      "value": "7A6"
    },
    "display": "ANEURIN BEVAN UNIVERSITY LHB"
  }
}

The FHIR API also supports search by a variety of parameters.

Let's search for general practices in Monmouth

$ curl -H "Accept: application/json" 'localhost:8080/fhir/Organization?address=monmouth&type=2.16.840.1.113883.2.1.3.2.4.17.507|RO177'

Or search for a named GP surgery:

$ curl -H "Accept: application/json" 'localhost:8080/fhir/Organization?name=Whitchurch&address=Wales&type=2.16.840.1.113883.2.1.3.2.4.17.507|RO177'

Development / contributing

Check for outdated dependencies:

$ clj -M:outdated

Perform compilation checks (optional)

$ clj -M:fhir-r4:serve:check

Perform linting (optional)

$ clj -M:lint/kondo
$ clj -M:lint/eastwood

Building and deploying the library

To generate a library jar:

clj -T:build jar

To install a library jar into your local maven repository:

clj -T:build install

To deploy the library to clojars:

clj -T:build deploy

Building executable files

If you prefer, you can generate jar files which can be run easily at the command line.

Build a server uberjar and run it. This provides a simple REST API.

$ clj -T:build http-server
$ java -jar target/clods-http-server-v1.0.152.jar /var/local/ods-2021-02 /var/local/nhspd-2020-11 8080

Build a FHIR server uberjar and run it. This provides a FHIR R4 server.

$ clj -T:build fhir-r4-server
$ java -jar target/clods-fhir-r4-server-1.0.152.jar /var/local/ods-2021-02 /var/local/nhspd-2020-11 8080

You can pass these standalone jar files around; they have no dependencies.

Copyright © 2020-22 Eldrix Ltd and Mark Wardle