rbbt-rest 1.3.32 → 1.4.0

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.3.32
+  version: 1.4.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-30 00:00:00.000000000 Z
+date: 2014-09-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -173,7 +173,6 @@ extra_rdoc_files:
 files:
 - LICENSE
 - Rakefile
-- config.ru
 - lib/rbbt/rest/client.rb
 - lib/rbbt/rest/client/adaptor.rb
 - lib/rbbt/rest/client/get.rb
@@ -220,8 +219,10 @@ files:
 - share/views/compass/favourites.sass
 - share/views/compass/figure.sass
 - share/views/compass/finder.sass
+- share/views/compass/fonts.sass
 - share/views/compass/foundation.sass
 - share/views/compass/functions.sass
+- share/views/compass/grid_system.sass
 - share/views/compass/help.sass
 - share/views/compass/layout.sass
 - share/views/compass/monitor.sass
@@ -1109,6 +1110,7 @@ files:
 - share/views/public/plugins/jquery/js/jquery-1.8.0.min.js
 - share/views/public/plugins/jquery/js/jquery-1.9.1.js
 - share/views/public/plugins/jquery/js/jquery-2.0.0.js
+- share/views/public/plugins/jquery/js/jquery-2.1.1.js
 - share/views/public/plugins/jquery/js/jquery.cookie.js
 - share/views/public/plugins/jquery/js/jquery.form.js
 - share/views/public/plugins/underscore/js/underscore.js

data/config.ru

@@ -1,102 +0,0 @@
-require 'zurb-foundation'
-require 'modular-scale'
-
-require 'sinatra'
-
-require 'rbbt'
-require 'rbbt/rest/main'
-require 'rbbt/rest/entity'
-require 'rbbt/rest/workflow'
-require 'rbbt/rest/file_server'
-require 'rbbt/rest/helpers'
-
-YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
-
-class RbbtRest < Sinatra::Base
-  
-  #{{{ MODULES AND HELPERS
-  register Sinatra::RbbtRESTMain
-  register Sinatra::RbbtRESTEntity
-  register Sinatra::RbbtRESTWorkflow
-  register Sinatra::RbbtRESTFileServer
-  helpers Sinatra::RbbtMiscHelpers
-
-  #{{{ DIRECTORIES
-  local_var = Rbbt.var.find(:lib)
-  set :cache_dir           , local_var.sinatra.cache.find
-  set :file_dir            , local_var.sinatra.files.find
-  set :favourites_dir      , local_var.sinatra.favourites.find
-  set :favourite_lists_dir , local_var.sinatra.favourite_lists
-
-  #{{{ SESSIONS
-  use Rack::Session::Cookie, :key => 'rack.session',
-    :path => '/',
-    :expire_after => 2592000,
-    :secret => 'StudyExplorer secret!!'
-
-  #{{{ FOUNDATION RESOURCES
-  add_sass_load_path "#{Gem.loaded_specs['compass'].full_gem_path}/frameworks/compass/stylesheets"
-  add_sass_load_path "#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/scss/" 
-  add_sass_load_path "#{Gem.loaded_specs['modular-scale'].full_gem_path}/stylesheets/" 
-  RbbtRESTHelpers.javascript_resources << Path.setup("#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/js/foundation")
-  RbbtRESTHelpers.javascript_resources << Path.setup("#{Gem.loaded_specs['zurb-foundation'].full_gem_path}/js/vendor")
-end
-
-#{{{ WORKFLOWS
-
-if Rbbt.etc.workflows.find(:lib).exists?
-  class RbbtRest
-    Rbbt.etc.workflows.find(:lib).read.split("\n").each do |workflow|
-      Workflow.require_workflow workflow
-      add_workflow Kernel.const_get(workflow), true
-    end
-  end
-end
-
-#{{{ ENTITIES
-
-require 'rbbt/entity'
-require 'rbbt/entity/genomic_mutation'
-require 'rbbt/entity/snp'
-require 'rbbt/entity/mutated_isoform'
-require 'rbbt/entity/chromosome_range'
-require 'rbbt/entity/study'
-require 'rbbt/entity/study/genotypes'
-require 'rbbt/entity/study/cnv'
-require 'rbbt/entity/study/methylation'
-
-require 'rbbt/sources/string'
-require 'rbbt/sources/pina'
-require 'rbbt/sources/go'
-require 'rbbt/sources/kegg'
-require 'rbbt/sources/InterPro'
-require 'rbbt/sources/pfam'
-require 'rbbt/sources/tfacts'
-
-$annotation_repo = Rbbt.var.find(:lib).cache.annotation_repo.find
-
-Entity.entity_list_cache = Rbbt.var.find(:lib).sinatra.entity_lists
-
-[Study, Sample, MutatedIsoform, GenomicMutation, SNP, ChromosomeRange, CNV, Gene, Protein, PMID, InterProDomain, KeggPathway, GOTerm, PfamDomain, NCINaturePathway, NCIReactomePathway, NCIReactomePathway].each do |mod|
-  mod.module_eval do
-    include Entity::REST
-  end
-end
-
-#{{{ FINDER
-class RbbtRest
-  finder = Finder.new
-  if production?
-   Thread.new do
-    #finder.add_instance(KEGG.pathways, :grep => "^hsa", :fields => ["Pathway Name"], :namespace => Organism.default_code("Hsa"))
-    #finder.add_instance(Organism.lexicon(Organism.default_code("Hsa")), :persist => true, :namespace => Organism.default_code("Hsa"), :grep => "^LRG_", :invert_grep => true)
-   end
-  end
-  set :finder, finder
-end
-
-#{{{ RUN
-$title = "RbbtRest"
-
-use Rack::Deflater
-run RbbtRest