code stringlengths 1 1.73M | language stringclasses 1
value |
|---|---|
##
blat = ARGV[0]
targeted = ARGV[1]
$gray = 200
$ranges = {}
File.new(targeted, 'r').each do |line|
if line=~ /^(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)/
tag, chr, offset, s,e =$1, $2, $3.to_i, $4.to_i, $5.to_i
ref = "chr" + chr
$ranges[ref] = [] unless $ranges.key?(ref)
$ranges[ref] << Range.ne... | Ruby |
## model:
## the duplicated regions must have:
## 1. significantly higher coverage than average
## 2. increase of "heterozygosity", i.e., the ratio of SNP reads / coverage is lower;
## 3. heterogenity of reads: the reads show SNPs have overall higher mismatch rate
## 4. tails
class Snp
attr_accessor :chr,... | Ruby |
##
$chromosome_change={"M"=>"DDB0169550","2F"=>"DDB0215018", "BF"=>"DDB0220052", "3F"=>"DDB0215151", "1"=>"DDB0232428", "2"=>"DDB0232429","3"=>"DDB0232430", "4"=>"DDB0232431", "5"=>"DDB0232432", "6"=>"DDB0232433"}
while line = ARGF.gets do
cols = line.split(/\s+/)
chr = cols[2]
if $chromosome_change.key... | Ruby |
## compute correlation coefficient between two lists of genes
# pseudo-code:
# sum_sq_x = 0
# sum_sq_y = 0
# sum_coproduct = 0
# mean_x = x[1]
# mean_y = y[1]
# for i in 2 to N:
# sweep = (i - 1.0) / i
# delta_x = x[i] - mean_x
# delta_y = y[i] - mean_y
# sum_sq_x += delta_x * delta_x * sweep
# sum_sq_y... | Ruby |
## given a SNP list from the whole genome and targeted genomic region, grab all the SNPs in the targeted region
## sorry, the format now is specifically for Dicty
require 'getoptlong'
opts = GetoptLong.new(
["--input", "-i", GetoptLong::REQUIRED_ARGUMENT],
["--target", "-t", GetoptLong::REQUIRED_ARGUMENT],... | Ruby |
## limit the length of each line to 80
input = ARGV[0]
output = input + '.mod.fa'
$fin = File.new(input, 'r')
$fout = File.new(output, 'w')
def format(seq)
return if seq == ''
s = seq.size
0.upto(s/80) do |i|
$fout.syswrite(seq[i*80..(i+1)*80-1] + "\n")
# $fout.syswrite(seq.slice!(0,80) + "\n")
end... | Ruby |
## call genotype after determine het_hom
while line=ARGF.gets do
cols=line.split(/\s+/)
if cols[9].to_f >= cols[5].to_f*0.9 # or cols[-1].to_f <0.01 # homo
gt = "#{cols[6]}#{cols[6]}"
else
# het
ref = cols[2].upcase
gt = [ref, cols[6]].sort.join()
end
puts "#{line.chomp}\t#{gt}"
end
| Ruby |
## convert encode info to a format that can be used for atlas-mapper-coverage.rb
# original format:
# ENm010 7 200000 27124046 27224045 BCM Old HOXA_cluster
# target format:
# target_name reference_name start_on_ref end_on_ref direction(1 or -1)
while line=ARGF.gets do
cols = line.s... | Ruby |
# simulate shotgun reads from reference genomes
require 'getoptlong'
opts = GetoptLong.new(
["--input", "-i", GetoptLong::REQUIRED_ARGUMENT],
["--coverage", "-c", GetoptLong::REQUIRED_ARGUMENT],
["--readSize", "-s", GetoptLong::OPTIONAL_ARGUMENT],
["--fixedSize", "-f", GetoptLong::OPTIONAL_ARGUMENT],
["--help", ... | Ruby |
## OLD: minor allele >20 % --> heterozygous SNP
## NEW: based on probability from binomial distribution
# Null hypothesis: the SNP is heterozygous, alterative: the SNP is homozygous.
## suggest Cutoff value: if Pr < 0.02, reject the null hypothesis ==> the SNP is homozygous.
def factorial(k)
if k <= 1
return... | Ruby |
##
# input format:
# ENm010 1955 9 chr7 27126000
def mean(a)
return -1 if a.size == 0
t = 0
a.map {|i| t+= i}
return t/a.size.to_f
end
pqueue = []
cqueue = []
while line = ARGF.gets do
cols = line.split(/\s+/)
name, pos, cov, chr, gpos = cols[0], cols[1].to_i, cols[2].to_i, cols[3... | Ruby |
## given a SNP list from the whole genome and targeted genomic region, grab all the SNPs in the targeted region
snplist = ARGV[0]
targeted = ARGV[1]
$gray = 200
$ranges = {}
File.new(targeted, 'r').each do |line|
if line=~ /^(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)/
tag, chr, offset, s,e =$1, $2, $3.to_i, $4.to_i... | Ruby |
##
realcc = ARGV[0]
simufof = ARGV[1]
hash = {}
avgs = {}
File.new(simufof, 'r').each do |line|
if line=~/^(\S+)/
ff = $1
File.new(ff,'r').each do |j|
if j=~ /^(\S+)\s+(\S+)\s+(\d+)/
gene, cc, ss = $1, $2, $3.to_i
if cc != 'NaN'
hash[gene] = [] unless hash.key?(gene)
... | Ruby |
# format reference sequence:
# 1. generate ooc file for BLAT
# 2. divide reference sequences into 100K overlapping pieces
## TODO:
# 1. consider circular genomes (microbes)
# Done 2. [perhaps] split huge genomes, such human genome,into smaller pieces for blat, in order to run BLAT with <=2G RAM.
require 'getoptlong'
... | Ruby |
require 'getoptlong'
opts = GetoptLong.new(
["--source", "-s", GetoptLong::REQUIRED_ARGUMENT],
["--list", "-l", GetoptLong::OPTIONAL_ARGUMENT],
["--name", "-n", GetoptLong::OPTIONAL_ARGUMENT],
# ["--qual", "-q", GetoptLong::NO_ARGUMENT],
["--output", "-o", GetoptLong::OPTIONAL_ARGUMENT],
["--he... | Ruby |
require 'zlib'
blatResult = ARGV[0]
$reads = {}
def processLine(line)
cols = line.split(/\s+/)
return if cols.size < 18
hit = {}
hit[:match], qgap,tgap,dir, query,qsize,hit[:qstart],hit[:qend],hit[:target],hit[:tsize],hit[:tstart],hit[:tend],hit[:blocks] =cols[0].to_i,cols[5].to_i,cols[7].to_i,cols[8],col... | Ruby |
## call genotypes at SNP sites based on Maximum Likelihood.
# the paramemter in question is the genotype.
require 'getoptlong'
opts = GetoptLong.new(
["--snp", "-s", GetoptLong::REQUIRED_ARGUMENT],
["--hapmap", "-m", GetoptLong::OPTIONAL_ARGUMENT],
["--help", "-h", GetoptLong::NO_ARGUMENT]
)
optHash = {... | Ruby |
## try to model the accurary of SNPs reported by single reads
snplist = ARGV[0]
# xm = ARGV[1]
transition = {'C' => 'T', 'A' => 'G', 'T' => 'C', "G" => 'A'}
snps = {}
num = 0
# count the occurence of homo-polymer runs in a short sequence
def homocount(str)
s = str.size
lasts = ''
homo = {}
st = 0
flag ... | Ruby |
## convert into a format that can be used by R to do glm or support vector machine
# features:
# 1. homopolymer size
# 2. original quality score
# 3. distance to 3' end
# 4. basechange type
# todo:
# upstream or downstream of homopolymer?
## base swap (consecutive or 1bp apart)?
trueS = ARGV[0]
falseS ... | Ruby |
##
str = []
n = 0
while line = ARGF.gets do
if line=~ /^(\d+)\s+/
s = $1.to_i
if s > n # choose one
puts str.sort_by {rand}[0]
n = s
str = []
end
str << line.chomp
end
end
| Ruby |
## input: cross_match -discrep_lists output
# note: this is for one-block alignment only
# ignoring 1bp indels
class Indel
attr_accessor :ref, :query, :tstart, :tend, :qstart, :qend, :dir,:sub, :dels,:ins,:envs, :type
def initialize(query, ref, qstart, qend, tstart, tend, dir,sub,dels,ins,l,envs,type)
@q... | Ruby |
## try to model the accurary of SNPs reported by single reads
snplist = ARGV[0]
# xm = ARGV[1]
transition = {'C' => 'T', 'A' => 'G', 'T' => 'C', "G" => 'A'}
snps = {}
num = 0
# count the occurence of homo-polymer runs in a short sequence
def homocount(str)
s = str.size
lasts = ''
homo = {}
st = 0
flag ... | Ruby |
# distribute the reads in a top-down fashion
fa = ARGV[0]
blatB = ARGV[1]
File.new(blatB, 'r').each do |line|
| Ruby |
## for longer homopolymer runs, make the first and last bases be the lowest quality
fa = ARGV[0]
qual = ARGV[1]
$order= []
$reads = {}
name = ''
File.new(fa, 'r').each do |line|
if line=~ /^>(\S+)/
name = $1
$reads[name] = {}
$order << name
$reads[name][:desc] = line.chomp
$reads[name][:s... | Ruby |
refList = ARGV[0]
File.new(refList, 'r').each do |line|
if line=~ /^(\S+)/
ref = $1
cmd = "time ruby ~/work/ruby/atlas-snp/atlas-mapper.rb -r #{ref} -q div_9.fa -z"
system(cmd)
end
end
| Ruby |
## compare SNP calls with Affy data
class Affy
attr_accessor :ref, :pos, :genotype, :alleles, :rs
def initialize(ref,pos,rs, gtype,alleles)
@ref, @pos, @genotype, @alleles,@rs = ref, pos, gtype, alleles,rs
end
end
require 'getoptlong'
opts = GetoptLong.new(
["--affy", "-a" , GetoptLong::REQUIRED_AR... | Ruby |
##
fa = ARGV[0]
ss = ARGV[1].to_i
pp = ARGV[2]
flags = {}
files = []
num = 1
fo = pp+'_'+num.to_s+ '.fa'
fout = File.new(fo, "w")
files << fo
seq = 0
File.new(fa,'r').each do |line|
if line=~ /^>(\S+)/
name = $1
if seq >= ss
flags[name] = 1
seq = 0
fout.close
num += 1
fo ... | Ruby |
## draw random 13-bp windows from the genome, to simulate "random" env for
| Ruby |
## input: cross_match -discrep_lists output
# limitations:
## 1. cross_match one-block alignment only
# 2. ignoring 1bp indels by default
# the quality of the indel:
# the accuracy of the gap size is important, therefore the quality of indels should reflect the confidence of the gap size
require 'getoptlong'... | Ruby |
##
prefix = ARGV[0] # prefix of output
ref = ARGV[1] # reference .bfa file
maps = ARGV[2..-1].join("\t") ## all the .map files, DIR/s*.map would do
# puts maps
# merge all .map files
system("maq mapmerge #{prefix}.map #{maps}")
# assemble
system("maq assemble #{prefix}.cns #{ref} #{prefix}.map 2> #{prefix}.c... | Ruby |
$maq = File.expand_path(`which maq`.chomp)
require 'getoptlong'
def main
optHash = getoptions()
if optHash.key?("--help")
help()
exit
end
dir = optHash["--dir"]
ref = optHash["--ref"]
flag = 1
log = "Maq.log"
maxMismatch = 3
maxDist = 250
## pe = findPairedEnds(dir)
pairedEndMapping(di... | Ruby |
# Author: Yufeng "Joshua" Shen
# split Solexa fastq into batches, each with 4 million lines
# (thus 1 million reads)
require 'getoptlong'
$maq = ''
def main
# logic of the program
maq = tryMaq()
if (maq == false)
exit
else
$maq = File.expand_path(maq)
end
optHash = getOptions() ## "--inputDir"... | Ruby |
# Author: Yufeng "Joshua" Shen
# convert solexa export file to fastq, and split into batches, each with 4 million lines
# (thus 1 million reads)
require 'getoptlong'
$maq = ''
def main
# logic of the program
maq = tryMaq()
if (maq == false)
exit
else
$maq = File.expand_path(maq)
end
optHash = ... | Ruby |
#!/usr/bin/env ruby
homeDir=Dir.pwd
#$stderr.puts homeDir
#homeDir=File.dirname(File.expand_path($1))
$stderr.puts homeDir
outputDir=homeDir+'/output/'
concensusDir=homeDir+'/consensus/'
inputDir=homeDir+'/input/'
parDir=homeDir+'/par/'
refDir=homeDir+'/references/'
#refDir=homeDir+'/references/'
file_pa... | Ruby |
require 'getoptlong'
require 'bigdecimal'
#Program overview
# 'atlasSNPEvaluate.rb' is used to evalute substitutions by looking at the posterior probability of
# a substitution site to be a true SNP (Posterior(SNP|Sj,Cov)j), which is appended in the last column of the output.
#
#Baysian's framework
# P... | Ruby |
#!/usr/bin/env ruby
require 'getoptlong'
require 'bigdecimal'
opts = GetoptLong.new(
["--input", "-i", GetoptLong::REQUIRED_ARGUMENT]
)
optHash = {}
opts.each do |opt, arg|
optHash[opt] = arg
end
homeDir=Dir.pwd
outputDir=homeDir+'/output/'
file_name=File.basename(optHash["--input"])
file_pat... | Ruby |
## parse gff or gtf file
# description of gff format: http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
# gtf: http://mblab.wustl.edu/GTF2.html
## <seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]
# DDB0232428 . gene 238722 242663 . + ... | Ruby |
# do blat and cross_match
require 'getoptlong'
opts = GetoptLong.new(
["--reference", "-r", GetoptLong::REQUIRED_ARGUMENT],
["--query", "-q", GetoptLong::REQUIRED_ARGUMENT],
# ["--output", "-o", GetoptLong::OPTIONAL_ARGUMENT],
["--minscore", "-m", GetoptLong::OPTIONAL_ARGUMENT],
["--cutoff", "-c", Ge... | Ruby |
# do blat and cross_match
require 'getoptlong'
opts = GetoptLong.new(
["--reference", "-r", GetoptLong::REQUIRED_ARGUMENT],
["--query", "-q", GetoptLong::REQUIRED_ARGUMENT],
# ["--output", "-o", GetoptLong::OPTIONAL_ARGUMENT],
["--minscore", "-m", GetoptLong::OPTIONAL_ARGUMENT],
["--cutoff", "-c", Ge... | Ruby |
# format reference sequence:
# 1. generate ooc file for BLAT
# 2. divide reference sequences into 100K overlapping pieces
## TODO:
# 1. consider circular genomes (microbes)
# 2. [perhaps] split huge genomes, such human genome,into smaller pieces for blat, in order to run BLAT with <=2G RAM.
require 'getoptlong'
opts... | Ruby |
# input: cross_match -discrep_lists output and the reference sequence
# output: 1. SNP list with useful information
# 2. a quality-like file storing coverage on each base of reference
# some part modified from Lei Chen's program
# only do substitutions
require 'getoptlong'
opts = GetoptLong.new(
["--cros... | Ruby |
# do blat and cross_match
require 'getoptlong'
opts = GetoptLong.new(
["--reference", "-r", GetoptLong::REQUIRED_ARGUMENT],
["--query", "-q", GetoptLong::REQUIRED_ARGUMENT],
# ["--output", "-o", GetoptLong::OPTIONAL_ARGUMENT],
["--minscore", "-m", GetoptLong::OPTIONAL_ARGUMENT],
["--cutoff", "-c", Ge... | Ruby |
# Copyright © 2010, EMC Corporation.
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# + Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... | Ruby |
require 'rubygems'
require 'rake/testtask'
require 'rake/gempackagetask'
task :default => [:gem]
spec = Gem::Specification.new do |s|
s.platform = Gem::Platform::RUBY
s.summary = "Ruby API wrapper for EMC Atmos"
s.name = 'atmos-ruby'
s.version = "1.4.0.7"
s.homepage = "http://code.google.com/p/atmos-ruby"
... | Ruby |
# Copyright © 2010, EMC Corporation.
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# + Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... | Ruby |
# This file should contain all the record creation needed to seed the database with its default values.
# The data can then be loaded with the rake db:seed (or created alongside the db with db:setup).
#
# Examples:
#
# cities = City.create([{ name: 'Chicago' }, { name: 'Copenhagen' }])
# Mayor.create(name: 'Emanuel... | Ruby |
class CreateArticles < ActiveRecord::Migration
def change
create_table :articles do |t|
t.string :title
t.text :text
t.timestamps null: false
end
end
end
| Ruby |
ENV['RAILS_ENV'] ||= 'test'
require File.expand_path('../../config/environment', __FILE__)
require 'rails/test_help'
class ActiveSupport::TestCase
# Setup all fixtures in test/fixtures/*.yml for all tests in alphabetical order.
fixtures :all
# Add more helper methods to be used by all tests here...
end
| Ruby |
source 'https://rubygems.org'
# Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
gem 'rails', '4.2.0'
# Use sqlite3 as the database for Active Record
gem 'sqlite3'
# Use SCSS for stylesheets
gem 'sass-rails', '~> 5.0'
# Use Uglifier as compressor for JavaScript assets
gem 'uglifier', '>= 1.3.0'
# Use Cof... | Ruby |
module WelcomeHelper
end
| Ruby |
module ApplicationHelper
end
| Ruby |
module ArticlesHelper
end
| Ruby |
class Article < ActiveRecord::Base
validates :title, presence: true, length: { minimum: 5 }
end
| Ruby |
class ApplicationController < ActionController::Base
# Prevent CSRF attacks by raising an exception.
# For APIs, you may want to use :null_session instead.
protect_from_forgery with: :exception
end
| Ruby |
class WelcomeController < ApplicationController
def index
end
end
| Ruby |
class ArticlesController < ApplicationController
def index
@articles = Article.all
end
def show
@article = Article.find(params[:id])
end
def new
end
def edit
end
def create
@article = Article.new(article_params)
@article.save
redirect_to @article
end
def update
end
def destroy
end... | Ruby |
# Be sure to restart your server when you modify this file.
# Add new inflection rules using the following format. Inflections
# are locale specific, and you may define rules for as many different
# locales as you wish. All of these examples are active by default:
# ActiveSupport::Inflector.inflections(:en) do |inflec... | Ruby |
# Be sure to restart your server when you modify this file.
# You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces.
# Rails.backtrace_cleaner.add_silencer { |line| line =~ /my_noisy_library/ }
# You can also remove all the silencers if you're trying to debug a probl... | Ruby |
# Be sure to restart your server when you modify this file.
# This file contains settings for ActionController::ParamsWrapper which
# is enabled by default.
# Enable parameter wrapping for JSON. You can disable this by setting :format to an empty array.
ActiveSupport.on_load(:action_controller) do
wrap_parameters f... | Ruby |
# Be sure to restart your server when you modify this file.
Rails.application.config.action_dispatch.cookies_serializer = :json
| Ruby |
# Be sure to restart your server when you modify this file.
# Version of your assets, change this if you want to expire all your assets.
Rails.application.config.assets.version = '1.0'
# Add additional assets to the asset load path
# Rails.application.config.assets.paths << Emoji.images_path
# Precompile additional ... | Ruby |
# Be sure to restart your server when you modify this file.
# Add new mime types for use in respond_to blocks:
# Mime::Type.register "text/richtext", :rtf
| Ruby |
# Be sure to restart your server when you modify this file.
Rails.application.config.session_store :cookie_store, key: '_blog_session'
| Ruby |
# Be sure to restart your server when you modify this file.
# Configure sensitive parameters which will be filtered from the log file.
Rails.application.config.filter_parameters += [:password]
| Ruby |
Rails.application.routes.draw do
get 'welcome/index'
resources :articles
# The priority is based upon order of creation: first created -> highest priority.
# See how all your routes lay out with "rake routes".
# You can have the root of your site routed with "root"
root 'welcome#index'
# Example of ... | Ruby |
ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
require 'bundler/setup' # Set up gems listed in the Gemfile.
| Ruby |
require File.expand_path('../boot', __FILE__)
require 'rails/all'
# Require the gems listed in Gemfile, including any gems
# you've limited to :test, :development, or :production.
Bundler.require(*Rails.groups)
module Blog
class Application < Rails::Application
# Settings in config/environments/* take preceden... | Ruby |
# Load the Rails application.
require File.expand_path('../application', __FILE__)
# Initialize the Rails application.
Rails.application.initialize!
| Ruby |
Rails.application.configure do
# Settings specified here will take precedence over those in config/application.rb.
# Code is not reloaded between requests.
config.cache_classes = true
# Eager load code on boot. This eager loads most of Rails and
# your application in memory, allowing both threaded web serve... | Ruby |
Rails.application.configure do
# Settings specified here will take precedence over those in config/application.rb.
# In the development environment your application's code is reloaded on
# every request. This slows down response time but is perfect for development
# since you don't have to restart the web serv... | Ruby |
Rails.application.configure do
# Settings specified here will take precedence over those in config/application.rb.
# The test environment is used exclusively to run your application's
# test suite. You never need to work with it otherwise. Remember that
# your test database is "scratch space" for the test suit... | Ruby |
# This file is used by Rack-based servers to start the application.
require ::File.expand_path('../config/environment', __FILE__)
run Rails.application
| Ruby |
# Add your own tasks in files placed in lib/tasks ending in .rake,
# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
require File.expand_path('../config/application', __FILE__)
Rails.application.load_tasks
| Ruby |
# $ext_path: This should be the path of where the ExtJS SDK is installed
# Generally this will be in a lib/extjs folder in your applications root
# <root>/lib/extjs
$ext_path = "../../"
# sass_path: the directory your Sass files are in. THIS file should also be in the Sass folder
# Generally this will be in a resource... | Ruby |
# include the utils rb file which has extra functionality for the ext theme
dir = File.dirname(__FILE__)
require File.join(dir, 'lib', 'utils.rb')
# register ext4 as a compass framework
Compass::Frameworks.register 'ext4', dir | Ruby |
# $ext_path: This should be the path of where the ExtJS SDK is installed
# Generally this will be in a lib/extjs folder in your applications root
# <root>/lib/extjs
$ext_path = "../../lib/extjs"
# sass_path: the directory your Sass files are in. THIS file should also be in the Sass folder
# Generally this will be in a... | Ruby |
module ExtJS4
module SassExtensions
module Functions
module Utils
def parsebox(list, n)
assert_type n, :Number
if !n.int?
raise ArgumentError.new("List index #{n} must be an integer")
elsif n.to_i < 1
raise ArgumentError.new("List index #{n} must... | Ruby |
# Add new inflection rules using the following format
# (all these examples are active by default):
# Inflector.inflections do |inflect|
# inflect.plural /^(ox)$/i, '\1en'
# inflect.singular /^(ox)en/i, '\1'
# inflect.irregular 'person', 'people'
# inflect.uncountable %w( fish sheep )
# end | Ruby |
# Add new mime types for use in respond_to blocks:
# Mime::Type.register "text/richtext", :rtf
# Mime::Type.register "application/x-mobile", :mobile | Ruby |
# Settings specified here will take precedence over those in config/environment.rb
# The production environment is meant for finished, "live" apps.
# Code is not reloaded between requests
config.cache_classes = true
# Use a different logger for distributed setups
# config.logger = SyslogLogger.new
# Full error repor... | Ruby |
# Settings specified here will take precedence over those in config/environment.rb
# In the development environment your application's code is reloaded on
# every request. This slows down response time but is perfect for development
# since you don't have to restart the webserver when you make code changes.
config.ca... | Ruby |
# Settings specified here will take precedence over those in config/environment.rb
# The test environment is used exclusively to run your application's
# test suite. You never need to work with it otherwise. Remember that
# your test database is "scratch space" for the test suite and is wiped
# and recreated between... | Ruby |
# Be sure to restart your web server when you modify this file.
# Uncomment below to force Rails into production mode when
# you don't control web/app server and can't set it the proper way
# ENV['RAILS_ENV'] ||= 'production'
# Specifies gem version of Rails to use when vendor/rails is not present
RAILS_GEM_VERSION ... | Ruby |
# Don't change this file. Configuration is done in config/environment.rb and config/environments/*.rb
RAILS_ROOT = "#{File.dirname(__FILE__)}/.." unless defined?(RAILS_ROOT)
unless defined?(Rails::Initializer)
if File.directory?("#{RAILS_ROOT}/vendor/rails")
require "#{RAILS_ROOT}/vendor/rails/railties/lib/init... | Ruby |
ActionController::Routing::Routes.draw do |map|
map.resources :interests, :member => {:order => :post}
map.resources :conferences
map.resources :users
map.resource :sessions
# The priority is based upon order of creation: first created -> highest priority.
# Sample of regular route:
# map.connect 'pr... | Ruby |
# Methods added to this helper will be available to all templates in the application.
module ApplicationHelper
end
| Ruby |
module UsersHelper
end | Ruby |
module SessionsHelper
end | Ruby |
module ConferencesHelper
end
| Ruby |
module InterestsHelper
end
| Ruby |
class Conference < ActiveRecord::Base
has_many :interests, :dependent => :destroy
end
| Ruby |
require 'digest/sha1'
class User < ActiveRecord::Base
has_many :interests, :order => 'position'
has_many :conferences, :through => :interests, :order => 'position'
# Virtual attribute for the unencrypted password
attr_accessor :password
validates_presence_of :login, :email
validates_presence_of ... | Ruby |
class Interest < ActiveRecord::Base
belongs_to :conference
def self.reorder(user, conference_ids)
transaction do
user.interests.destroy_all
conference_ids.each_with_index do |conference_id, n|
user.interests.create! :conference_id => conference_id, :position => n+1
end
end
end... | Ruby |
class ConferencesController < ApplicationController
before_filter :login_required
# GET /conferences
# GET /conferences.xml
def index
@conferences = Conference.find :all
@my_conferences = current_user.conferences
@conferences = @conferences - @my_conferences
respond_to do |format|
format... | Ruby |
class InterestsController < ApplicationController
before_filter :login_required
# GET /interests
# GET /interests.xml
def index
@interests = Interest.find(:all)
respond_to do |format|
format.html # index.html.erb
format.xml { render :xml => @interests }
end
end
# GET /interests/1... | Ruby |
# This controller handles the login/logout function of the site.
class SessionsController < ApplicationController
# Be sure to include AuthenticationSystem in Application Controller instead
include AuthenticatedSystem
# render new.rhtml
def new
end
def create
self.current_user = User.authenticate(pa... | Ruby |
# Filters added to this controller apply to all controllers in the application.
# Likewise, all the methods added will be available for all controllers.
class ApplicationController < ActionController::Base
helper :all # include all helpers, all the time
include AuthenticatedSystem
end
| Ruby |
class UsersController < ApplicationController
# render new.rhtml
def new
end
def create
@user = User.new(params[:user])
@user.save!
self.current_user = @user
redirect_back_or_default('/')
flash[:notice] = "Thanks for signing up!"
rescue ActiveRecord::RecordInvalid
render :action => 'n... | Ruby |
# Add your own tasks in files placed in lib/tasks ending in .rake,
# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
require(File.join(File.dirname(__FILE__), 'config', 'boot'))
require 'rake'
require 'rake/testtask'
require 'rake/rdoctask'
require 'tasks/rails'
| Ruby |
#!/usr/bin/env ruby
require File.dirname(__FILE__) + '/../config/boot'
require 'commands/console' | Ruby |
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