Installation and Execution of MediCurator

You can easily install Mediurator with only a few staps.

First, you need to get a copy of MediCurator from the following website https://bitbucket.org/BMI/medicurator. Here is the quick start.

Set the Constants

Basicly, the user should set the following the arguments.

  1. Set the API_KEY in ./config.sh
  2. Set DATA_BASE_DIR in ./src/main/java/edu/emory/bmi/medicurator/Constants.java
  3. Set PROXY_HOST, PROXY_PORT if necessary.

The user can choose use HdfsStorage or LocalStorage by changing STORAGE (hdfs/local) in Constants.java. To use HDFS, you should config HDFS_URI and HDFS_BASEDIR in Constants.java. For example, HDFS_URI = “hdfs://localhost:9000/” and HDFS_BASEDIR = “/user/xxx/medicurator/”

Building and Executing Using Apache Maven 3.3.x

Building

$./compile.sh

Testing

$mvn test

Run web application

$./run_servlet.sh

It is expected to have the TCIA_API_KEY set in the Constants.java to build with tests.

The webapp runs at http://localhost:2222/Index

You may want to run

$mvn exec:java -Dexec.mainClass=”edu.emory.bmi.medicurator.infinispan.StartInfinispan”

first so that data you hava stored beforehand won’t be lost although the web server has been closed.

Run Restful API

$./run_api.sh

Extend or leverage the exposed APIs, or simply test using a REST client such as the Postman Chrome application.

Dependencies

This project depends on the below major projects.

  1. Infinispan 8.2 stable
  2. dcm4che 3
  3. Apache HTTP Client
  4. Tomcat 7
  5. Hadoop 2.7.2
  6. Spark Java 2.5
Have feedback or corrections? Email us at chen1ru@pku.edu.cn.