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

QTakes - Apache cTAKES™ REST API on Quarkus
https://github.com/dermatologist/quick-ctakes

ctakes ctakes-clinical-pipeline docker docker-compose quarkus rest-api

Last synced: 24 days ago
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QTakes - Apache cTAKES™ REST API on Quarkus

• Host: GitHub
• URL: https://github.com/dermatologist/quick-ctakes
• Owner: dermatologist
• Created: 2020-03-02T15:41:20.000Z (over 4 years ago)
• Default Branch: develop
• Last Pushed: 2023-04-17T17:41:34.000Z (over 1 year ago)
• Last Synced: 2024-10-03T19:10:51.395Z (about 1 month ago)
• Topics: ctakes, ctakes-clinical-pipeline, docker, docker-compose, quarkus, rest-api
• Language: Java
• Homepage: http://nuchange.ca
• Size: 95.7 KB
• Stars: 7
• Watchers: 3
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

        
# :rocket: QTakes - Apache cTAKES™ on Quarkus

![quick-ctakes](https://forthebadge.com/images/badges/made-with-java.svg)

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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](https://github.com/apache/ctakes). 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](https://github.com/GoTeamEpsilon/ctakes-rest-service). 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