katerose / encoded

Metadata database for ENCODE 3

ENCODE Metadata Database

Note: the default Mac python doesn't seem to work. You might want to install Python with Homebrew and you may need to install one of more of (using homebrew): libxml2 libxslt freetype openssl libjpeg.

First run buildout:

$ python2.7 bootstrap.py
$ bin/buildout

To start the application:

$ bin/pserve development.ini

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

Run the Jasmine tests at http://localhost:6543/tests/js/test_runner.html.

Run the Pyramid tests with:

$ bin/test -k -bdd

Run the Browser tests with:

$ bin/test -k bdd -v -v

To run tests with sqllite (default) use:

$ bin/test --engine-url sqlite://

To run tests with postgresql::

first install postgres (on a mac with homebrew for example)

If you wish a clean db wipe for DEVELOPMENT $ dropdb encoded ... $ createdb encoded $ pg_ctl -D postgres -l pg.log start $ bin/test --engine-url postgresql:///encoded

To start development data server (NO PERMISSIONS) use:

$bin/pserve development.ini

To start development data server (AuthZ enabled) use:

(requires ../master_encode3_interface_submissions.xlsx) $bin/pserve dev-master.ini

To start productiondata server (Postgres, AuthZ, all data) use:

(requires ../master_encode3_interface_submissions.xlsx and/or existing PG DB) $bin/pserve production.ini

$bin/pserve --help for more pyramid options --log-file [filename] is a useful argument

Database setup on VMs:

# service postgresql-9.2 initdb
# service postgresql-9.2 start
# sudo -u postgres createuser --createdb encoded

Then as the encoded user:

$ createdb encoded

Notes on SASS/Compass

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).

Installing

Both can be installed via Ruby gems:

$ gem install sass
$ gem install compass

Compiling "on the fly"

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.)

Force compiling

$ 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