search

dot-base / icd-10-api

Rest API to search the 10th revision of the International Statistical Classification of Diseases Database.
GNU General Public License v3.0
18 stars 4 forks source link
fhir icd-10 nodejs-server rest-api

readme

ICD-10 API (German Version) ⚕️🔟

API to search the german version of the 10th revision of the International Statistical Classification of Diseases Database.

GitHub release (latest by date)

Contents

  1. Production Deployment
  2. Configuration
  3. Considerations
  4. Setup for Local Development

Production Deployment

Want an ICD-10 api of your own? The easiest way is to deploy our docker container. Just follow the steps below to get started.

Docker Build Status

Requirements

Deployment

  1. Set environment variables to configure the container: 
    export MAX_SEARCH_WORDS="6"
  2. Start the container with a single command 
    docker run --name icd-10-api -p 3000:3000 -d ghcr.io/dot-base/icd-10-api:latest
  3. Done and dusted 🎉. The ICD-10 api is available on port 3000.

Usage

Submit a GET request to /api/icd10 using the search query parameter:

'Parkinson-Syndrom Primär' -> http://localhost:3000/api/icd10?search=Parkinson-Syndrom%20Prim%C3%A4r

Configuration

Environment Variables

Variable Name Default Example
MAX_SEARCH_WORDS 6 -

Considerations

Pre-processing and multi-term searches

The ICD-10 api processes a search query by first splitting it into separate search terms as in the following example:

'Parkinson-Syndrom Primär' -> ['Parkinson', 'Syndrom', Primär]
'Parkinson G20.9 unspezifisch' -> ['Parkinson', 'G20.9', 'unspezifisch']

If a query consists of several terms, the ICD-10 api will assemble all combinations of these terms and order them by length:

'Parkinson-Syndrom Primär' -> ['Parkinson Syndrom Primär', 'Parkinson Syndrom', 'Parkinson Primär', 'Syndrom Primär', 'Parkinson', 'Syndrom', 'Primär']

The service will search for matches in descending order, meaning it will first search for the full term 'Parkinson Syndrom Primär'. If no match was found, the search will proceed with 'Parkinson AND Syndrom' 'Parkinson AND Primär' 'Syndrom AND Primär'. If the combination of two search terms results in one or several matches, the search will stop and return the result. Otherwise, it will proceed to search for each single term separately. Due too performance and time-out reasons the default max. value for search terms is set to 6, but can be changed indiviually by setting MAX_SEARCH_WORDS.

Prioritization of ICD-10 codes

Terms that match the ICD code pattern are handled with priority. If a query contains something like 'Parkinson G20' or 'Parkinson G20.9', the service will first try to find exact matches for these ICD codes. It will only search for further results matching 'Parkinson', if no matching ICD codes were found.

Setup for Local Development

The following steps need to be done only once. After that, you are ready to deploy a dot.base stack with very little commands for testing and development.

Install prerequisits

You will need bash, coreutils, docker, git, mkcert, openssl, sudo and watch.

Checkout this repository

Checkout the dot.base repository and move into it.

git clone git@github.com:dot-base/icd-10-api.git
cd icd-10-api

Generate a Github personal access token

Some components of the dot.base stack are private. So you need to generate a Github personal access token for an account that has access to private dot.base repositories. The token needs the right to write:packages/read:packages. Go to https://github.com/settings/tokens/new?scopes=write:packages to generate it.

Login with your access token

Use YOUR_TOKEN and YOUR_GITHUB_USERNAME to login to the container registry.

export CR_PAT=<YOUR_TOKEN>
echo $CR_PAT | docker login ghcr.io -u <YOUR_GITHUB_USERNAME> --password-stdin

Deploy a stack with one service overlayed for development

In order to develop a service in its complete dot.base environment, you need to deploy the complete dot.base stack and replace the service you want develop with a dev overlay (a dev container containing the toolchains required for develpment). All dot.base services contain a launch-stack.sh.

❗ This requires root!

./launch-stack.sh

Install service dependencies

docker exec -it $(docker ps -q -f name=dotbase_icd-10-api) npm install

Start this service in development mode

docker exec -it $(docker ps -q -f name=dotbase_icd-10-api) npm start

Watch your dot.base stack

./dot-base/dot-base.sh watch

Observe logs

./dot-base/dot-base.sh logs

Stats

docker stats

Use it

Just checkout the dot.base instance on https://${APP_HOSTNAME}, e.g. https://dotbase.local

You need to accept the security exception once in your browser as we are using a self-signed certificate.

Add a user

You'll want to add a user in keycloak's dotbase realm via the Keycloak Admin panel. https://${APP_HOSTNAME}/auth, e.g. https://dotbase.local/auth

Username: admin Password: password.

Stop the stack

./dot-base/dot-base.sh stop

Cleanup

To undo initial setup, run:

❗ This requires root!

./dot-base/dot-base.sh cleanup

To cleanup dockers cache of images and containers run the following.

❗ Be sure to know what you are doing. This deletes on your whole docker instance, not only on the dot.base stack! This is destructive!

docker images prune --all
docker container prune --all

To cleanup dockers volumes, which will reset all databases, including dot.base FHIR data and keycloak user data, run the following.

❗ Be sure to know what you are doing. This deletes on your whole docker instance, not only on the dot.base stack! This is destructive!

docker volumes prune --all

To cleanup all of dockers data, run the following.

❗ Be sure to know what you are doing. This deletes on your whole docker instance, not only on the dot.base stack! This is destructive!

docker system prune --all