KingFisher

Tumor Heterogeneity Analysis and Visualization Tool

Updates

-02/06/2015 : Establish basic framework for testing. Provided basic documentation. Working landing page. -15/06/2015 : Added Hiercherical Clustering Service at the server backend. Added Service to store data at the from end dataFactory. -16/06/2015 : Added Parser for Maf and Clinical Data -19/06/2015 : Boxplot, line plot and phylogenetic tree. Example dataset.

Introduction

OncoBlocks is a new open-source project, initiated by the Dana-Farber Cancer Institute and Memorial Sloan Kettering Cancer Center. The goal of the project is to create reusable, open source software components to support cancer genomics research and enable precision (or "personalized") cancer medicine.

Project KingFisher a component of Oncoblock and is web-based prototype for visualizing and analyzing multiple genomic snapshots over time and space.

Dependencies

1. SQL Database - Currently KingFisher is running on MySQL. Other dialects of SQL might work but have not been tested yet.
2. Java - KingFisher have only been tested on Java 8.
3. Maven - KingFisher have only been tested on maven3 ( 3.3.3 to be specific)

Getting Started - Introduction

Kingfisher is a Java Spring-boot application currently configured to work with SQL databases. To configure your database settings please edit application.properties file found in src/main/resources. For more information regarding configuration of the application.properties please refer to guide By default, kingfisher will use the following environment variable for your database settings.

1. $sql_address - address of your mysql server. for eg. localhost/kfisher
2. $sql_user - username for connecting to your MySQL server e.g. kingfisheruser
3. $sql_pass - password used to access the MySQL.

Building / Testing KingFisher

KingFisher uses JUnit and Jasmine for testing.

To test kingfisher - do the following

mvn test - There are a total of 4 tests and 2 Jasmine Specs. Make sure your database is running

To run Jasmine Test alone

mvn jasmine:bdd - This will launch server that binds to port 8234 on the localhost localhost:8234

Jasmine test on the command is not working at the momemnt

To build kingfisher

mvn build - This will generate a war file in target/ . It should have the following filename: kingfisherboot-X.X.X.RELEASE.war where X.X.X refer to the version number of the application.

To run Kingfisher

mvn spring-boot:run this will run kingfisher locally using the Spring boot maven plugin

For Deployment

Pop your war file into your tomcat webapp directory

For more information about deploying applications. Please refer to tomcat documentation or have a look at cbioportal's wiki page

Route map

Verb	Path	Status	Response	Description
GET	/	200	index.html	src/main/resources/template/index.html
GET	/prototype	200	prototype.html	src/main/resources/template/prototype.html
GET	/rest	200	application/json	JSON object of all entries in database
POST	/rest	200	xhr	Post data
GET	/js/*	200	*.js	javascript libraries
GET	/hclust	200	Do hiercherical clustering	newick format representing hiercherical clustering results