fabfile.py

from __future__ import with_statement

from fabric.api import cd, env, local, run
from fabric.colors import green
from fabric.contrib.files import exists

from server import create_app
from server.db import mongo, Disease, Finding, FindingWeight

import server.parseFile as parseFile

env.user = 'athlabs'
env.hosts = [ 'labs.athlabs.com' ]

PROJECT_NAME   = 'doknosis'
PRODUCTION_DIR = 'doknosis.athlabs.com'
GIT_LOCATION   = 'gitolite@igert8.ucsd.edu:doknosis.git'

COFFEE_IN   = 'coffeescript'
COFFEE_OUT  = 'static/js'

SASS_IN     = 'sass/layout.scss'
SASS_OUT    = 'static/css/layout.css'


def compile():
    '''
        Compile and minify JS and CSS sources.

        JS is compiled using Coffeescript
        CSS is compiled using SASS
    '''
    compile_js()
    compile_css()


def compile_js():
    print green( 'Compiling coffeescript into javascript...' )
    local( 'coffee -b -j doknosis.coffee -o %s -c %s' %
            ( COFFEE_OUT, COFFEE_IN ) )


def compile_css():
    print green( 'Compiling sass into css...' )
    local( 'sass --update -t compressed %s:%s' % ( SASS_IN, SASS_OUT ) )


def fill_db():
    '''
        Fill the database ( should be EMPTY ) based on the findings/disease CSV
        file
    '''
    # Create an app context so we can access the database
    app = create_app()
    mongo.init_app( app )
    with app.test_request_context():

        # Parse CSV file and grab the findings/disease lists
        print green( 'Parsing disease/finding CSV file...' )
        tbl = parseFile.createCSVTable()
        findings, diseasesList = parseFile.createDiseaseList(tbl)

        # Used to associate a finding name to the database object
        print green( 'Adding findings to database...' )

        # Add findings to database
        for obj in findings:
            fname = obj.strip().lower()

            if Finding.query.filter( {'name': fname} ).count() == 0:
                finding = Finding( name=fname )
                finding.save()

        # Add diseases to database
        print green( 'Adding diseases to database...' )
        for obj in diseasesList:

            disease = Disease( name=obj.name )

            # Findings are represented as [ Finding name, weight ]
            for fw in obj.findings:
                fname   = fw[ 0 ].strip().lower()
                weight  = float( fw[ 1 ] )

                disease.findings.append( FindingWeight( name=fname,
                                                      weight=weight ) )

            disease.save()