meikeric / ctakes-rest-service

A JSON-based rest service to process unstructured clinical text through a smart natural language processing system.

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.

Install

(Based on Ubuntu 18)

1. Install Java 8 and MySQL 5.7 (reference)

sudo apt-get update
sudo apt-get install default-jdk
sudo apt-get install mysql-server

Set the 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

2. 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

3. Install Maven 3.5, Subversion, and Git.

sudo apt-get install maven
sudo apt-get install subversion
sudo apt-get install git

4. Git clone this repository: git clone https://github.com/GoTeamEpsilon/ctakes-rest-service.git.
5. 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 ..

6. cd into 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'

7. 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

8. Navigate back to the main codebase and build:

cd ../../../ctakes-web-rest
mvn install

9. 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

10. Access the URL http://localhost:8080/ctakes-web-rest/index.jsp for testing the REST service. This should return a default index page.

11. 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).

License

Apache License, Version 2.0