website for BRCA challenge

To contribute: Fork the repository, make the changes, and submit pull request.

Build the frontend

The build is based on npm and webpack.

• Ensure that git and node are installed
  • On OSX, install brew http://brew.sh/
    • brew install git
    • brew install node
  • On Linux:
    • sudo apt-get install git-all
    • curl -sL https://deb.nodesource.com/setup_5.x | sudo -E bash -
    • sudo apt-get install -y nodejs
• Checkout the repo
  • git clone https://github.com/BD2KGenomics/brca-website.git
• Start the frontend
  • cd brca-website
  • npm install
  • npm start

Build the server

The server runs on Django with postgres so install and set up those

• Install postgres
  • For Mac:
    • The easiest way is to install postgress.app from http://postgresapp.com/
  • Linux:
    • sudo apt-get install postgresql postgresql-contrib
• Create the database
  • sudo -u postgres createdb storage.pg
• Set the postgres role's password
  • sudo -u postgres psql postgres
  • at the prompt type \password postgres to set the password to postgres
• Install the python dependencies
  • pip install -qU -r requirements.txt
• Run the initial migration to populate the database
  • cd django
  • python manage.py migrate
• Start the server
  • python manage.py runserver
• If you're developing locally point the frontend at the local server
  • Edit databaseUrl in js/backend.js to point to localhost:8000
• Browse to http://localhost:8080/

Lint

Use npm run lint to run the lint rules. We lint with eslint and babel-eslint.

How to change the data file

This process will delete all the previous data from the variants table and replace it with data from a new tsv file.

• Replace the contents of data/resources/aggregated.tsv with the new data file
• (Optional step if the schema has changed) Change the following files to correspond to schema changes (renamed / added / removed columns)
  • django/data/models.py - this is the python model that corresponds to all the table columns
  • django/data/migrations/0001_initial.py - specifies all the table columns, it matches the model above and the tsv headers
  • django/data/migrations/0002_search_index.py - specifies which columns are used in full text search
  • (if applicable) django/data/migrations/0004_autocomplete_words.py - specifies which columns are used in autocomplete suggestions
  • js/VariantTable.js:
    • columns specifies which columns appear in the default mode and their names
    • research_mode_columns specifies which columns appear in research mode and their names
    • subColumns specifies which columns appear in the column selection filter and how they're grouped.
• cd django
• python manage.py migrate --fake data zero && python manage.py migrate

References

• http://blog.keithcirkel.co.uk/how-to-use-npm-as-a-build-tool/
• http://webpack.github.io/
• http://www.youtube.com/watch?v=VkTCL6Nqm6Y