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b0c9a6e
fix typo
May 14, 2014
019b48d
adding lc to checks with specific gender requirements
May 23, 2014
1ad5e98
making sure aliases are strings
May 23, 2014
ea378cf
local repository
May 23, 2014
c784488
remove lc
May 28, 2014
c3f5e0a
local gms versions
May 28, 2014
72c49ce
Merge branch 'master' of /proj/famgen/git/gms
May 28, 2014
04098f1
updated sweepers to reset ped_info and all_pedigrees calls on after_save
Jun 11, 2014
8dcc4fd
change ped_info for people to be arrays because collaborator_ids aka
Jun 12, 2014
c0fc859
remove spaces from collaborator id
Jul 14, 2014
e447314
updating study page to show number of genomes
Jul 23, 2014
0651088
add chartkick
Jul 28, 2014
e37cc2b
update the production output to be in /proj/famgen/gms
Oct 15, 2014
c5610b3
make ids that are floats into strings
Apr 7, 2015
8c4cc7b
add expire people
Apr 7, 2015
0c38d28
fix for if there's no root person
Apr 7, 2015
82cef4c
added exception for the wellness study to the
Apr 9, 2015
ec9775c
Updating ruby versions
Oct 7, 2016
1626f79
Fixes for ruby 2.3.1
Oct 7, 2016
aea8bad
Updated to prevent missing template errors
Oct 7, 2016
c20b1b0
Fix circos handling
Oct 7, 2016
34858b4
Merge remote-tracking branch 'isb/master'
denisemauldin Jun 8, 2020
7292d64
Update to Rails 6 and Ruby 2.7.0
denisemauldin Jun 8, 2020
f9e0fb3
Update scopes, collection_selects, and html formatting
denisemauldin Jun 10, 2020
73e24e5
Fix export pathname
denisemauldin Jun 10, 2020
562a069
update capistrano settings
Jun 11, 2020
656037c
Session Migration
Jun 11, 2020
460a8cd
Update pedigree loading and displaying
denisemauldin Jun 15, 2020
3e83066
Add image to assets
denisemauldin Jun 15, 2020
ae52fca
Fix get_drop_down_samples_by_pedigree
denisemauldin Jun 15, 2020
89f371b
fix finds and expire_action
denisemauldin Jun 26, 2020
8df5263
Upgrade to Rails 6 asset handling. Add Bootstrap and use bootstrap t…
denisemauldin Jun 26, 2020
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1 change: 1 addition & 0 deletions .browserslistrc
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
defaults
62 changes: 47 additions & 15 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,19 +1,51 @@
.bundle/*
db/*.sqlite3
log/*.log
tmp/
vendor/*
# See https://help.github.com/articles/ignoring-files for more about ignoring files.
#
# If you find yourself ignoring temporary files generated by your text editor
# or operating system, you probably want to add a global ignore instead:
# git config --global core.excludesfile '~/.gitignore_global'

# Ignore bundler config.
/.bundle
bin/*

# Ignore the default SQLite database.
/db/*.sqlite3
/db/*.sqlite3-journal
/db/*.sqlite3-*

# Ignore all logfiles and tempfiles.
/log/*
log/*
/tmp/*
tmp/*
!/log/.keep
!/tmp/.keep

# Ignore pidfiles, but keep the directory.
/tmp/pids/*
!/tmp/pids/
!/tmp/pids/.keep

# Ignore uploaded files in development.
/storage/*
!/storage/.keep

/public/assets
.byebug_history

# Ignore master key for decrypting credentials and more.
/config/master.key

/public/packs
/public/packs-test
/public/pedigrees
/node_modules
/yarn-error.log
yarn-debug.log*
.yarn-integrity

data/*
public/pedigrees/*
%*
.%*
?
*save
*old
._*
#*
.#*
config/cap_user.rb
vendor/*
config/database.yml
config/ldap.yml
config/database.yml.example
Expand Down
2 changes: 1 addition & 1 deletion .ruby-version
Original file line number Diff line number Diff line change
@@ -1 +1 @@
ruby-1.9.3-p448
ruby-2.7.0@rails6
41 changes: 38 additions & 3 deletions Capfile
Original file line number Diff line number Diff line change
@@ -1,4 +1,39 @@
load 'deploy' if respond_to?(:namespace) # cap2 differentiator
Dir['vendor/gems/*/recipes/*.rb','vendor/plugins/*/recipes/*.rb'].each { |plugin| load(plugin) }
# Load DSL and set up stages
require "capistrano/setup"

load 'config/deploy' # remove this line to skip loading any of the default tasks
# Include default deployment tasks
require "capistrano/deploy"

# Load the SCM plugin appropriate to your project:
#
# require "capistrano/scm/hg"
# install_plugin Capistrano::SCM::Hg
# or
# require "capistrano/scm/svn"
# install_plugin Capistrano::SCM::Svn
# or
require "capistrano/scm/git"
install_plugin Capistrano::SCM::Git

# Include tasks from other gems included in your Gemfile
#
# For documentation on these, see for example:
#
# https://github.com/capistrano/rvm
# https://github.com/capistrano/rbenv
# https://github.com/capistrano/chruby
# https://github.com/capistrano/bundler
# https://github.com/capistrano/rails
# https://github.com/capistrano/passenger
#
require "capistrano/rvm"
# require "capistrano/rbenv"
# require "capistrano/chruby"
require "capistrano/bundler"
require "capistrano/rails/assets"
# require "capistrano/rails/migrations"
#require "capistrano/passenger"
require "whenever/capistrano"

# Load custom tasks from `lib/capistrano/tasks` if you have any defined
Dir.glob("lib/capistrano/tasks/*.rake").each { |r| import r }
182 changes: 97 additions & 85 deletions Gemfile
Original file line number Diff line number Diff line change
@@ -1,88 +1,100 @@
source 'http://rubygems.org'

gem 'rails'
gem 'rake'
gem 'builder'
gem 'net-ssh', '~>2.7.0'
#gem 'net-ssh', '~> 2.8.1', :git => "https://github.com/net-ssh/net-ssh"
gem 'debugger'

gem 'aws-sdk'
# Bundle edge Rails instead:
# gem 'rails', :git => 'git://github.com/rails/rails.git'
gem 'mysql2'
gem 'minitest'

# Use unicorn as the web server
# gem 'unicorn'

# Deploy with Capistrano
#gem 'rvm-capistrano'
#gem 'capistrano-bundler'
#gem 'capistrano-rails'
gem 'capistrano', '~> 2.15.5'
# To use debugger (ruby-debug for Ruby 1.8.7+, ruby-debug19 for Ruby 1.9.2+)
# gem 'ruby-debug'
#gem 'linecache19', :git => "git://github.com/mark-moseley/linecache"
#gem 'ruby-debug-base19x', "~>0.11.30.pre10"
#gem 'ruby-debug19', :require => 'ruby-debug'

gem 'settingslogic'

gem 'strong_parameters'

gem 'will_paginate'
gem 'jquery-rails'#, '~> 2.1'
gem 'select2-rails' # jquery select boxes
gem 'formtastic'
gem 'event-calendar', :require => 'event_calendar'
gem 'simple_navigation'
gem 'gollum' # wiki

#gem 'devise'
#gem 'devise_ldap_authenticatable'
#gem 'cancan'
gem 'attr_encrypted'

gem 'paperclip'
gem 'spreadsheet'
#gem 'princely'

gem 'ancestry'
#gem 'awesome_nested_set'
#gem 'acts_as_audited'
#, "2.0.0.rc7"

gem 'madeline', '~> 0.1.11'

gem 'rubyzip', '<1.0.0'
gem 'auto_strip_attributes'#, "~> 1.0"
gem 'json_builder'

# create cron jobs to clean the temporary objects from the database
gem 'whenever'
gem 'rspec-rails'

# testing
source 'https://rubygems.org'
git_source(:github) { |repo| "https://github.com/#{repo}.git" }

ruby '2.7.0'

# Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
gem 'rails', '~> 6.0.3', '>= 6.0.3.1'
# Use Puma as the app server
gem 'puma', '~> 4.1'
# Use SCSS for stylesheets
gem 'sass-rails', '>= 6'
# Transpile app-like JavaScript. Read more: https://github.com/rails/webpacker
gem 'webpacker', '~> 4.0'
# Turbolinks makes navigating your web application faster. Read more: https://github.com/turbolinks/turbolinks
gem 'turbolinks', '~> 5'
# Build JSON APIs with ease. Read more: https://github.com/rails/jbuilder
gem 'jbuilder', '~> 2.7'
# Use Redis adapter to run Action Cable in production
# gem 'redis', '~> 4.0'
# Use Active Model has_secure_password
# gem 'bcrypt', '~> 3.1.7'

# Use Active Storage variant
# gem 'image_processing', '~> 1.2'

# Reduces boot times through caching; required in config/boot.rb
gem 'bootsnap', '>= 1.4.2', require: false

group :development, :test do
# Call 'byebug' anywhere in the code to stop execution and get a debugger console
gem 'byebug', platforms: [:mri, :mingw, :x64_mingw]
end

group :development do
# Access an interactive console on exception pages or by calling 'console' anywhere in the code.
gem 'web-console', '>= 3.3.0'
gem 'listen', '~> 3.2'
# Spring speeds up development by keeping your application running in the background. Read more: https://github.com/rails/spring
gem 'spring'
gem 'spring-watcher-listen', '~> 2.0.0'
end

group :test do
gem 'factory_girl'
gem 'factory_girl_rails'
gem 'shoulda'
gem 'shoulda-matchers'
gem 'fakefs', :require => "fakefs/safe"
gem "database_cleaner"
gem "email_spec"
# Adds support for Capybara system testing and selenium driver
gem 'capybara', '>= 2.15'
gem 'selenium-webdriver'
# Easy installation and use of web drivers to run system tests with browsers
gem 'webdrivers'
end

# Bundle the extra gems:
# gem 'bj'
# gem 'nokogiri'
# gem 'sqlite3-ruby', :require => 'sqlite3'
# gem 'aws-s3', :require => 'aws/s3'

# Bundle gems for the local environment. Make sure to
# put test-only gems in this group so their generators
# and rake tasks are available in development mode:
# group :development, :test do
# gem 'webrat'
# end
# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]

gem "list", "~> 0.2.0"

gem "activerecord-session_store", "~> 1.1"

gem "actionpack-action_caching", "~> 1.2"
gem "actionpack-page_caching", "~> 1.2"
gem "rails-observers", "~> 0.1.5"

gem "aws-sdk", "~> 3.0"

gem "mysql2", "~> 0.5.3"

gem "responders", "~> 3.0"

gem "capistrano-bundler", "~> 1.6"
gem "capistrano-passenger", "~> 0.2.0"
gem "capistrano", "~> 3.14"
gem "capistrano-rails", "~> 1.5"
gem "capistrano-rvm", "~> 0.1.2"

gem "settingslogic", "~> 2.0"

gem "will_paginate", "~> 3.3"

gem "paperclip", "~> 6.1"

gem "spreadsheet", "~> 1.2"

gem "ancestry", "~> 3.0"

gem "rubyzip", "~> 2.3"

gem "auto_strip_attributes", "~> 2.6"

gem "json_builder", "~> 3.1"

gem "whenever", "~> 1.0"

gem "rspec-rails", "~> 4.0"

gem "builder", "~> 3.2"

gem "madeline", "~> 0.1.11"

gem "jquery-tablesorter", "~> 1.27"

gem "jquery-turbolinks", "~> 2.1"
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