Welcome to the wiki of the MEDIator - Data Replication System project!

Please visit the website to learn more - https://bitbucket.org/BMI/datareplicationsystem

Set the API_KEY, MASHAPE_AUTHORIZATION, and BASE_UR as environment variables.

For example, in Linux.

export API_KEY=your-api-key

export MASHAPE_AUTHORIZATION=your-mashape-authorization

export BASE_URL=services.cancerimagingarchive.net/services/v4/TCIA/query

 mvn package

It is expected to have the TCIA API_KEY set in the environment variables to build with tests.

If you do not have a TCIA API_KEY yet, please build with skipping the tests.

mvn package -DskipTests

 sh modules/repl-server/target/bin/webapp

Go to http://localhost:9090/mediator/ using your browser to access the Data Replication and Synchronization Tool.

Make sure to include log4j2-test.xml into your class path to be able to configure and view the logs. Default log level is [WARN].

This project depends on the below major projects.

• Infinispan
• Apache Tomcat (Embedded)
• Apache HTTP Client
• Apache Velocity
• Apache Log4j2
• Mashape Unirest

[1.1] TCIA Programmatic Interface (REST API) Usage Guide - https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide

[1.2] TCIA on Mashape - https://www.mashape.com/tcia/the-cancer-imaging-archive

[1.3] TCIA REST API Client - https://github.com/nadirsaghar/TCIA-REST-API-Client

[2.1] Using MongoDB as cache store - http://blog.infinispan.org/2013/06/using-mongodb-as-cache-store.html

[2.2] Infinispan MongoDB Cache Store - https://github.com/infinispan/infinispan-cachestore-mongodb

If you prefer to use an EC2 Instance to upload clinical files to S3, you may follow the below steps.

Otherwise, you may directly upload the clinical files which were downloaded to your local computer.

• Connect to the instance

$ ssh -i pradeeban.pem [email protected]

• Make a directory and change to the directory.

$ mkdir gsoc2014

$ cd gsoc2014

• Download and extract the meta data from the online repository (link sent to email. Given below is an example).

$ nohup wget https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/userCreatedArchives/652ccf44-cfda-4e99-81ac-d8f4c0eca6be.tar > nohup.out &

$ tar -zxvf 652ccf44-cfda-4e99-81ac-d8f4c0eca6be.tar

If you wish to reproduce the system in another deployment, please refer to documentation/HOW-TO.