🚀 QTakes - Apache cTAKES™ on Quarkus

Apache cTAKES™ is a natural language processing system for the extraction of information from electronic medical record clinical free-text. A web application providing REST API for cTAKES is available from the original repository. This is an extension of the REST API using Quarkus, (the Supersonic Subatomic Java Framework) designed for containers (docker).

04/10/2021: Updated with cTakes patch 4.0.0.1 for UmlsKey

You need

• docker
• java 8
• maven

How to use

STEP 1: Create the database

You can use a local or remote MySQL database. The SQL data scripts are available in this repo. Refer to the section titled 'SQL Data Scripts.' You can also spin up a docker container with these scripts as below (Yes, it has to be MySQL 5):

FROM mysql:5

COPY ./sno_rx_16ab_db/ /docker-entrypoint-initdb.d/

STEP 2: Check out this repo and add the details

git clone https://github.com/dermatologist/quick-ctakes.git

Add the database details in customDictionary.xml in the resources folder. Make changes to the Default.piper if needed

STEP 3: Build the java application, test it and package it

cd quick-ctakes
./mvnw clean compile quarkus:dev
mvn clean package -DskipTests

STEP 4: Dockarize it

• See the docker folder for details

docker build -f src/main/docker/Dockerfile.jvm -t <docker-user/container-name:tag .

• A sample docker-compose is also provided. (Add UMLS KEY HERE)

STEP 5: Use as below

curl -X POST -H "Content-Type: text/plain" --data "this is hypertension and diabetes" 127.0.0.1:8080/analyze

More about Quarkus

This project uses Quarkus, the Supersonic Subatomic Java Framework.

If you want to learn more about Quarkus, please visit its website: https://quarkus.io/ .

Running the application in dev mode

You can run your application in dev mode that enables live coding using:

./mvnw quarkus:dev

Packaging and running the application

The application is packageable using ./mvnw package. It produces the executable quick-ctakes-1.0.0-SNAPSHOT-runner.jar file in /target directory. Be aware that it’s not an über-jar as the dependencies are copied into the target/lib directory.

The application is now runnable using java -jar target/quick-ctakes-1.0.0-SNAPSHOT-runner.jar.

Creating a native executable

You can create a native executable using: ./mvnw package -Pnative.

Or you can use Docker to build the native executable using: ./mvnw package -Pnative -Dquarkus.native.container-build=true.

You can then execute your binary: ./target/quick-ctakes-1.0.0-SNAPSHOT-runner

If you want to learn more about building native executables, please consult https://quarkus.io/guides/building-native-image-guide .