A JSON-based rest service to process unstructured clinical text through a smart natural language processing system.
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danehrlich1 secured Spring Framework with latest 4.3.x Version
upgraded Spring Framework to latest 4.x version, which appears to be 4.3.18 (from 4.3.10).

See here: https://spring.io/blog/2018/06/13/spring-framework-5-0-7-and-4-3-18-available-now

They will support Version 4 until 2020, so at some point Version 5 should be moved to as well.
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README.md

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.

img

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

  1. 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
  1. Install Maven 3.5, Subversion, and Git.
sudo apt-get install maven
sudo apt-get install subversion
sudo apt-get install git
  1. Git clone this repository: git clone https://github.com/GoTeamEpsilon/ctakes-rest-service.git.
  2. 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 ..
  1. 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'
  1. 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
  1. Navigate back to the main codebase and build:
cd ../../../ctakes-web-rest
mvn install
  1. 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
  1. Access the URL http://localhost:8080/ctakes-web-rest/index.jsp for testing the REST service. This should return a default index page.

  2. 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