De-identification Docker Image

by the Medical College of Wisconsin and MSOE

The following code is used to deidentify data from the following incoming data sets :

• Database
• Flat files ( coming soon )
• HDFS ( coming soon )

After de-identification the data can be written back to a remote database or to a local Postgres instance .

Requirements

One needs to have the following installed to run this software

• Docker ( 1.12.* in Beta at this time)
• git
• Runs on mac only ( bat scripts coming soon)

Docker can be installed from their website. To install git we suggest installing Homebrew

Then install git with the command :

brew install git

Setup

First download the Linux JDK jdk-8u111-linux-i586.tar.gz at the time of this writing and put it into the archive directory .

From : http://www.oracle.com/technetwork/java/javase/downloads/index.html If a differennt version is present then one will need to update the install_java.sh script to reference that one.

No matter if one is running a standalone or Local database one needs to first pull down the git repo of deid software . This is done with by running :

./build.sh

This pulls down the recent software and builds the local container .

Running

Standalone

With to local Postgres instance

In this instance we use docker-compose to start up both the "app" and the "db" with processing going into the postgres db from the app.

Configutation

Before one begins the de-id process one needs to set up where one gets the incoming data and where it's going to .

s = "Python syntax highlighting"
print s

Limitations / Configuration