rbbt-rest 1.3.29 → 1.3.30

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data/config.ru CHANGED
@@ -88,8 +88,8 @@ class RbbtRest
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  finder = Finder.new
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  if production?
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  Thread.new do
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- #finder.add_instance(KEGG.pathways, :grep => "^hsa", :fields => ["Pathway Name"], :namespace => "Hsa/jun2011")
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- #finder.add_instance(Organism.lexicon("Hsa/jun2011"), :persist => true, :namespace => "Hsa/jun2011", :grep => "^LRG_", :invert_grep => true)
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+ #finder.add_instance(KEGG.pathways, :grep => "^hsa", :fields => ["Pathway Name"], :namespace => Organism.default_code("Hsa"))
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+ #finder.add_instance(Organism.lexicon(Organism.default_code("Hsa")), :persist => true, :namespace => Organism.default_code("Hsa"), :grep => "^LRG_", :invert_grep => true)
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  end
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  end
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  set :finder, finder
@@ -27,7 +27,7 @@ module RbbtRESTHelpers
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  name += "_" << Misc.hash2md5(params) if params.any?
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- path = File.join(settings.cache_dir, name)
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+ path = settings.cache_dir[name].find
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  task = Task.setup(:name => "Sinatra cache", :result_type => :string, &block)
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  step = Step.new(path, task, nil, nil, self)
@@ -33,7 +33,7 @@ module RbbtRESTHelpers
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  def serve_js(compress = true)
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  if production? and compress and not @debug_js
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  md5 = Misc.digest(recorded_js_files * ",")
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- filename = File.join(settings.file_dir, "all_js-#{md5}.js")
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+ filename = settings.file_dir["all_js-#{md5}.js"].find
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  if not File.exists?(filename)
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  Log.debug{ "Regenerating JS Compressed file: #{ filename }" }
@@ -33,10 +33,6 @@ module Sinatra
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  base.module_eval do
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  helpers EntityRESTHelpers
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- set :favourites_dir, Rbbt.var.find.sinatra.favourites
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- set :favourite_lists_dir, Rbbt.var.find.sinatra.favourite_lists
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- set :favourite_maps_dir, Rbbt.var.find.sinatra.favourite_maps
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- set :finder, nil
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36
 
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  get /^\/entity.*/ do
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  @cache_type = :asynchronous if @cache_type.nil?
@@ -71,7 +71,7 @@ module EntityRESTHelpers
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  dir = Path.setup(File.join(settings.favourite_lists_dir, user))
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  if (file = dir[entity_type]).exists?
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- lists = Open.read(file).split("\n")
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+ lists = Open.read(file.find).split("\n")
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  lists << list
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  Open.write(file, lists.uniq * "\n")
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  else
@@ -39,7 +39,7 @@ module KnowledgeBaseRESTHelpers
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  user = "guest" if user.nil?
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  @@user_knowledge_bases ||= IndiferentHash.setup({})
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  @@user_knowledge_bases[user] ||= begin
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- kb = KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, File.join('user', user)), "Hsa/jan2013"
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+ kb = KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, File.join('user', user)), Organism.default_code("Hsa")
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  kb.format["Gene"] = "Ensembl Gene ID"
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  kb.syndicate Genomics.knowledge_base, :genomics
@@ -20,9 +20,9 @@ module Sinatra
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  add_sass_load_path Rbbt.share.views.compass.find(:lib)
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- set :cache_dir, Rbbt.var.sinatra.cache.find unless settings.respond_to? :cache_dir and settings.cache_dir != nil
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- set :file_dir, Rbbt.var.sinatra.files.find unless settings.respond_to? :file_dir and settings.file_dir != nil
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- set :permalink_dir, Rbbt.var.sinatra.permalink.find unless settings.respond_to? :permalink_dir and settings.permalink_dir != nil
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+ #set :cache_dir, Rbbt.var.sinatra.cache.find unless settings.respond_to? :cache_dir and settings.cache_dir != nil
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+ #set :file_dir, Rbbt.var.sinatra.files.find unless settings.respond_to? :file_dir and settings.file_dir != nil
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+ #set :permalink_dir, Rbbt.var.sinatra.permalink.find unless settings.respond_to? :permalink_dir and settings.permalink_dir != nil
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  set :public_folder, Rbbt.share.views.public.find
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metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: rbbt-rest
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  version: !ruby/object:Gem::Version
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- version: 1.3.29
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+ version: 1.3.30
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
9
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  bindir: bin
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  cert_chain: []
11
- date: 2014-08-15 00:00:00.000000000 Z
11
+ date: 2014-08-26 00:00:00.000000000 Z
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12
  dependencies:
13
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  - !ruby/object:Gem::Dependency
14
14
  name: rake