A JSON-based rest service to process unstructured clinical text through a smart natural language processing system.
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ctakes-web-rest addressing security vulnerability Oct 17, 2018
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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.

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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
mysqladmin -u root password pass

The above sets the root password to pass. You can also use custom configurations and specify them in ./ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml.

Note: This repo assumes you installed MySQL on the default port 3066

  1. Install Tomcat 8 using the detailed instructions here)

  2. 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 ./sno_rx_16ab_db
for fname in *.sql; do sudo mysql -u root < $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 issuting 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