Beacon queries and interface for the MongoDB based arrayMap cancer genome repository.

The structure of the project is the following:

mongo-queries:

Queries are contained inside the directory mongo-queries

Download commands

The following command can be used to download a chunk of the arrayMap dataset, e.g. to understand data structures.

wget "http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata&randno=200" -O 200samples.json

The next command would replace the current local arrayMap instance with the downloaded file.

mongoimport --drop --db arraymap --collection samples < 200samples.json --batchSize 1

beacon-app

The directory contains the Beacon application itself.

The application is based on node and angular.

In order to run the application on your localhost, you need to have npm installed.

Then, run:

npm install

in order to get all the required Javascript packages (as listed in package.json), and then:

npm start

You should also have a arrayMap MongoDB running on your localhost, on port 27017 (see above).

This can be changed in the application container:

app.js

bin

Contains the www script which is used by

npm start

to start the server.

arraymap-beacon

Contains the implementation of the Beacon API. There is one sub-directory per API version.

test

Contains the functional tests (based on the Chai assertion library).

public

Contains the scripts, CSS, images, HTML for the UI part.

routes

Contains the routing script.

views

Contains jade files. Jade is used as a view engine to display nice error pages in case an error is thrown (instead of raw stacktraces).