_

Step 1: Verify that homebrew is working properly:

$ brew doctor

Step 2: Install or update dependencies:

$ brew install libevent libmagic libxml2 libxslt elasticsearch openssl postgresql node graphviz
$ brew install freetype libjpeg libtiff littlecms webp  # Required by Pillow

Note: For Mac < 10.9, the system python doesn't work. You should install Python with Homebrew:

$ brew install python

If you need to update dependencies:

$ brew update
$ brew upgrade
$ rm -rf encoded/eggs

Step 3: Run buildout:

$ python2.7 bootstrap.py -v 2.2.5 --setuptools-version 7.0
$ bin/buildout

If you see a clang error like this:

clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]

You can try:

$ ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future bin/buildout

If it does not exist, set a session key:

$ cat /dev/urandom | head -c 256 | base64 > session-secret.b64

Step 4: Start the application locally

In one terminal startup the database servers with:

$ bin/dev-servers development.ini --app-name app --clear --init --load

This will first clear any existing data in /tmp/encoded. Then postgres and elasticsearch servers will be initiated within /tmp/encoded. The servers are started, and finally the test set will be loaded.

In a second terminal, run the app in with:

$ bin/pserve development.ini

Indexing will then proceed in a background thread similar to the production setup.

Browse to the interface at http://localhost:6543/.

Step 5: Tests

To run specific tests locally:

$ bin/test -k test_name

To run with a debugger:

$ bin/test --pdb 

Specific tests to run locally for schema changes:

$ bin/test -k test_load_workbook
$ bin/test -k test_edw_sync

Run the Pyramid tests with:

$ bin/test -m "not bdd"

Run the Browser tests with:

$ bin/test -m bdd -v -v

Run the Javascript tests with:

$ npm test

Or if you need to supply command line arguments:

$ ./node_modules/.bin/jest

Step 6: Database modifications

If you wish a clean db wipe for DEVELOPMENT:

$ dropdb encoded
...
$ createdb encoded
$ pg_ctl -D /usr/local/var/postgres -l pg.log start

Database setup on VMs:

# service postgresql-9.3 initdb
# service postgresql-9.3 start
# sudo -u postgres createuser --createdb encoded

Then as the encoded user:

$ createdb encoded

To dump a postgres database:

pg_dump -Fc encoded > FILE_NAME (as user encoded on demo vm) (FILE_NAME for production is ~/encoded/archive/encoded-YYYYMMDD.dump)

To restore a postgres database:

pg_restore -d encoded FILE_NAME (as user encoded on demo vm)

Create ElasticSearch mapping for ENCODE data:

$ bin/create-mapping production.ini

SASS and Compass are being used. Before running to app, you need to builld the css files by starting 'compass watch' or doing a 'compass compile' (see below).

Both can be installed via Ruby gems:

$ gem install sass
$ gem install compass

Compass can watch for any changes made to .scss files and instantly compile them to .css. To start this, from the root of the project (where config.rb is) do:

$ compass watch

You can specify whether the compiled CSS is minified or not in config.rb. (Currently, it is set to minify.)

$ compass compile

Again, you can specify whether the compiled CSS is minified or not in config.rb.

Also see the Compass Command Line Documentation and the Configuration Reference.

And of course:

$ compass help

To setup SublimeLinter with Sublime Text 3, first install the linters:

$ easy_install-2.7 flake8
$ npm install -g jshint
$ npm install -g jsxhint

After first setting up Package Control (follow install and usage instructions on site), use it to install the following packages in Sublime Text 3:

• sublimelinter
• sublimelinter-flake8
• sublimelinter-jsxhint
• jsx
• sublimelinter-jshint