cTAKES Rest Service
The goal of this solution is to provide a JSON-based REST service to process unstructured clinical text through a smart natural language processing system in a fast, accurate, and easy to setup way.
(Based on Ubuntu 18)
- Install Java 8 and MySQL 5.7 (reference)
sudo apt-get update sudo apt-get install default-jdk sudo apt-get install mysql-server
root password to
pass. Use the instructions here if you are not prompted during setup.
Note: This repo assumes you installed MySQL on the default port 3066
- Install Tomcat 8 using the detailed instructions here). Some important points:
- Open the inbound 8080 port so you can access from a browser using the instructions here.
- Increase the java heap size by running
sudo vi /opt/tomcat/latest/bin/setenv.sh, including the line
CATALINA_OPTS="$CATALINA_OPTS -Xms5120m -Xmx5120m"and saving.
- Restart your machine to make sure Tomcat picks up the new settings
- Install Maven 3.5, Subversion, and Git.
sudo apt-get install maven sudo apt-get install subversion sudo apt-get install git
- Git clone this repository:
git clone https://github.com/GoTeamEpsilon/ctakes-rest-service.git.
- Load in all SQL scripts in
./sno_rx_16ab_db. This process may take several hours.
cd ctakes-rest-service/sno_rx_16ab_db for fname in *.sql; do sudo mysql -u root -ppass < $fname; done cd ..
cdinto the repository and run the following to pull down cTAKES:
mkdir ctakes-codebase-area cd ctakes-codebase-area svn export 'https://svn.apache.org/repos/asf/ctakes/trunk'
- Build the appropriate cTAKES modules with the following:
cd trunk/ctakes-distribution mvn install -Dmaven.test.skip=true cd ../ctakes-assertion-zoner mvn install -Dmaven.test.skip=true
- Navigate back to the main codebase and build:
cd ../../../ctakes-web-rest mvn install
- Deploy the War file:
sudo mv target/ctakes-web-rest.war /opt/tomcat/latest/webapps/ # useful for debugging (uncomment): # tail -f /opt/tomcat/latest/logs/catalina.out
Access the URL
http://localhost:8080/ctakes-web-rest/index.jspfor testing the REST service. This should return a default index page.
Test the installation by issuing a POST request to
http://localhost:8080/ctakes-web-rest/service/analyze?pipeline=Default. You can do this using a client like Postman (remember to use the POST method and RAW response).
Apache License, Version 2.0