SparkStreamingCTK

Introduction

An example of using the ClinicalPipeline project adding the ability to utilize Spark Streaming.

Prerequisites

• Download and install Apache cTAKES v3.2.2 as shown below. It is important to install v3.2.2 as this is expected later on.

$ cd /usr/local
$ wget "http://archive.apache.org/dist/ctakes/ctakes-3.2.2/apache-ctakes-3.2.2-bin.tar.gz"
$ tar -zxvf apache-ctakes-3.2.2-bin.tar.gz

• Download and install ClinicalPipeline. WARNING - This installation takes a LONG time. Go and make yourself a cup of tea!

$ cd /usr/local
$ git clone https://github.com/giuseppetotaro/ctakes-clinical-pipeline.git
$ cd ctakes-clinical-pipeline
$ mvn install 

Installation

Update CtakesFunction.java with UMLS username and password. The case be obtained by registering with and signing the UMLS Metathesaurus License. Once you have it, proceeed as below:

$ vim src/main/java/org/dia/red/ctakes/spark/CtakesFunction.java

Then populate the following two properties with your username and password respectively:

	private void setup() throws UIMAException {
		System.setProperty("ctakes.umlsuser", "");
		System.setProperty("ctakes.umlspw", "");

Then build the project.

$ mvn install

Running the Spark Streaming Service Locally

$ cd target
$ tar -zxzf spark-ctakes-0.1-dist.tar.gz
$ cd spark-ctakes-0.1/bin
$ ./start-ctakes-server.sh 9321

This will start the streaming service which you can now interact with. We provide an example below.

Client Example

This is an example displaying how we can submit portions of clinical text to the streaming service using netcat. First we need to obtain some sample data, this can be located in the file sampledata.tar.gz

$ tar -zxvf sampledata.tar.gz

We can then use netcat to submit this data over TCP/IP to the local service. The service uses the UMLS credentials provided earlier to process the input data.

$ nc 127.0.0.1 9321 < sampledata/all.txt

Executing on an Existing Spark Cluster

When we installed the project as above, you may have also noticied that besides the generated spark-ctakes-0.1-dist.tar.gz and spark-ctakes-0.1-dist.zip artifacts, the build system also generated an spark-ctakes-0.1-job.jar artifact.

This artifact is a self-contained job JAR (uber jar) that contains all the dependencies required to run our application on an existing Cluster.

The Spark Documentation provides excellent context on how to submit your jobs. A bare bones example is provided below:

• Typical syntax using spark-submit

./bin/spark-submit \
  --class <main-class>
  --master <master-url> \
  --deploy-mode <deploy-mode> \
  --conf <key>=<value> \
  ... # other options
  <application-jar> \
  [application-arguments]

Now an example for our application

$ ./bin/spark-submit \
  --class org.dia.red.ctakes.spark.CtakesSparkMain \
  --master spark://207.184.161.138:7077 \
  --executor-memory 20G \
  --total-executor-cores 100 \
  target/spark-ctakes-0.1-job.jar \
  sampledata/all.txt

License

SparkStreamingCTK is licensed under the Apache License v2.0. A copy of that license is shipped with this source code.