Source Code

Overview

All source code may be found on the ICGC DCC GitHub repository.

Projects

Common Libraries (dcc-common)

Common Libraries GitHub repository

Reusable software modules used throughout the ICGC DCC projects described here.

Installation System (dcc-cm)

Configuration Management GitHub repository

Installation automation and configuration management (CM) system for DCC operational environments.

This project includes Ansible playbooks for provisioning ETL, Portal, Downloader and Submission systems as well as docker containers for provisioning software on docker hosts.

Storage System (dcc-storage)

Storage System GitHub repository

Software for uploading and downloading ICGC files in cloud environments. This system powers ICGC in the Cloud.

Submission System (dcc-submission)

Submission System GitHub repository

Software for accepting and validating ICGC clinical and experimental data files. This system powers https://submissions.dcc.icgc.org/ and provides the main input to the ETL system.

Data Download (dcc-download)

Data Download GitHub repository

Software component for Downloading data used by the Data Portal. Contains the client code as well the server which allows to download data over HTTPS.

Data Portal (dcc-portal)

Portal GitHub repository

Project powering the ICGC Data Portal used for exploring, visualizing, and downloading ICGC data.

The repository contains the source code which powers the Data Portal's API, UI, as well as the underlying query infrastructure.

Docs (dcc-docs)

Docs GitHub repository

Source code for this site. Powered by mkdocs and GitHub Pages.

Release (dcc-release)

Release GitHub repository

Parent project for all the modules that make up the Release(ETL) pipeline for transforming project submissions into Data Portal products.

ID (dcc-id)

ID GitHub repository

The ID project is used by DCC ETL project to obfuscate sensitive clinical data. It generates surrogate IDs for submitted clinical data which are then used in the Data Portal.

Import (dcc-import)

Import GitHub repository

Project which contains all the import modules used for importing reference data for use by the ETL pipeline. Imported data is staged in MongoDB.

Repository (dcc-repository)

Repository GitHub repository

Importer for the ICGC "Data Repository" feature which imports file metadata from various external data repositories.

iobio (dcc-iobio)

iobio GitHub repository

The ICGC customized iobio containers for accessing ICGC cloud based files. Currently contains the ICGC customized bam.iobio container.

Major changes over the base iobio container are related to security improvements and integration of the ICGC Storage Client.

Parent (dcc-parent)

Parent POM GitHub repository

This project provides shared configuration for Maven builds for use in ICGC DCC projects.