rbbt-rest 1.3.29 → 1.3.30

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 569bc3bd7ef12134107f7a9d86e328c8ff8f4a31
-  data.tar.gz: 62defeb01c385abea3649e46417abe60e4c67500
+  metadata.gz: 70eadc019665982b6532c66001097037f05aa48f
+  data.tar.gz: 714e805b544731a3bbd8131cd89afe359f3cfcf1
 SHA512:
-  metadata.gz: 11ca1a3a88efe3d724d9d257defc9b897e5dca2ffabd839ad892aada831701f978043863c8bb6ae4d45b6303fc7ffffcf0881fd7d40220956ce45458f4db850a
-  data.tar.gz: eb31418e346e1875ac4be8bb1e57b04cffac25c56898289e838187ed01f0cea3434532c0545e3ca97b50eec8e9ec4f335f7752c54441d74f912317da0c302051
+  metadata.gz: c0e871bebff8a59fbedcebd28719f17cdca4a1be53a3db53a505419f4c363f0bb8951cef0fabe9b28d583992259cd8cba1c0ccf0682deb2e0b102cdccce4c546
+  data.tar.gz: f3b3b9168038e51817a6dec862686aa42917a6a6f087c3350d180336774356edd7db22f1c11c03e317c3c3056fac989c64231d9bb1cac58205e82f6b0ca29638

data/config.ru

@@ -88,8 +88,8 @@ class RbbtRest
   finder = Finder.new
   if production?
    Thread.new do
-    #finder.add_instance(KEGG.pathways, :grep => "^hsa", :fields => ["Pathway Name"], :namespace => "Hsa/jun2011")
-    #finder.add_instance(Organism.lexicon("Hsa/jun2011"), :persist => true, :namespace => "Hsa/jun2011", :grep => "^LRG_", :invert_grep => true)
+    #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

data/lib/rbbt/rest/common/cache.rb

@@ -27,7 +27,7 @@ module RbbtRESTHelpers
     
     name += "_" << Misc.hash2md5(params) if params.any?
 
-    path = File.join(settings.cache_dir, name)
+    path = settings.cache_dir[name].find
     task = Task.setup(:name => "Sinatra cache", :result_type => :string, &block)
 
     step = Step.new(path, task, nil, nil, self)

data/lib/rbbt/rest/common/resources.rb

@@ -33,7 +33,7 @@ module RbbtRESTHelpers
   def serve_js(compress = true)
     if production? and compress and not @debug_js 
       md5 = Misc.digest(recorded_js_files * ",")
-      filename = File.join(settings.file_dir, "all_js-#{md5}.js")
+      filename = settings.file_dir["all_js-#{md5}.js"].find
 
       if not File.exists?(filename)
         Log.debug{ "Regenerating JS Compressed file: #{ filename }" }

data/lib/rbbt/rest/entity.rb

@@ -33,10 +33,6 @@ module Sinatra
       base.module_eval do
         helpers EntityRESTHelpers
 
-        set :favourites_dir, Rbbt.var.find.sinatra.favourites
-        set :favourite_lists_dir, Rbbt.var.find.sinatra.favourite_lists
-        set :favourite_maps_dir, Rbbt.var.find.sinatra.favourite_maps
-        set :finder, nil
 
         get /^\/entity.*/ do
           @cache_type = :asynchronous if @cache_type.nil?

data/lib/rbbt/rest/entity/favourites.rb

@@ -71,7 +71,7 @@ module EntityRESTHelpers
     dir = Path.setup(File.join(settings.favourite_lists_dir, user))
 
     if (file = dir[entity_type]).exists?
-      lists = Open.read(file).split("\n")
+      lists = Open.read(file.find).split("\n")
       lists << list
       Open.write(file, lists.uniq * "\n")
     else

data/lib/rbbt/rest/knowledge_base/helpers.rb

@@ -39,7 +39,7 @@ module KnowledgeBaseRESTHelpers
     user = "guest" if user.nil?
     @@user_knowledge_bases ||= IndiferentHash.setup({})
     @@user_knowledge_bases[user] ||= begin
-                                       kb = KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, File.join('user', user)), "Hsa/jan2013"
+                                       kb = KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, File.join('user', user)), Organism.default_code("Hsa")
                                        kb.format["Gene"] = "Ensembl Gene ID"
 
                                        kb.syndicate Genomics.knowledge_base, :genomics

data/lib/rbbt/rest/main.rb

@@ -20,9 +20,9 @@ module Sinatra
 
         add_sass_load_path Rbbt.share.views.compass.find(:lib)
 
-        set :cache_dir, Rbbt.var.sinatra.cache.find unless settings.respond_to? :cache_dir and settings.cache_dir != nil
-        set :file_dir, Rbbt.var.sinatra.files.find unless settings.respond_to? :file_dir and settings.file_dir != nil
-        set :permalink_dir, Rbbt.var.sinatra.permalink.find unless settings.respond_to? :permalink_dir and settings.permalink_dir != nil
+        #set :cache_dir, Rbbt.var.sinatra.cache.find unless settings.respond_to? :cache_dir and settings.cache_dir != nil
+        #set :file_dir, Rbbt.var.sinatra.files.find unless settings.respond_to? :file_dir and settings.file_dir != nil
+        #set :permalink_dir, Rbbt.var.sinatra.permalink.find unless settings.respond_to? :permalink_dir and settings.permalink_dir != nil
 
         set :public_folder, Rbbt.share.views.public.find 
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.3.29
+  version: 1.3.30
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-15 00:00:00.000000000 Z
+date: 2014-08-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake