working version with proxy

1 files changed, 44 insertions, 50 deletions

diff --git a/application.rb b/application.rb
index 68bb8d2..9162fcf 100644
--- a/application.rb
+++ b/application.rb
@@ -1,25 +1,21 @@
+require "./pug.rb"
 require "./pubchem.rb"
-require 'rack/session/dalli'
-require "rack/cache"
 module OpenTox
-  class Application < Service
+  class Application < Sinatra::Base
+
     set :static, true
     set :root, File.dirname(__FILE__)
-    also_reload './pubchem.rb'
-
-    @@pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
 
-    before do
-      #cache_control :public, :max_age => 3600
+    configure :development do
+      register Sinatra::Reloader
+      also_reload './pubchem.rb'
     end
 
     before '/cid/:cid/*' do
-      #cache_control :public, :max_age => 3600
-      session[:compound] = PubChemCompound.new params[:cid] unless session[:compound] and session[:compound].cid == params[:cid]
+      @compound = PubChemCompound.new params[:cid] 
     end
 
     get '/?' do
-      #cache_control :public, :no_cache
       haml :index
     end
 
@@ -28,58 +24,71 @@ module OpenTox
     end
 
     get '/search/?' do
-      #cache_control :public, :no_cache
-      begin
-        cids = RestClient.get(File.join(@@pug_uri,"compound","name",CGI.escape(params[:name]),"cids","TXT")).split("\n")
-        if cids.size == 1
-          session[:compound] = PubChemCompound.new cids.first
-          haml :compound
-        elsif cids.size > 1
-          @compounds = cids.collect{|cid| PubChemCompound.new cid }
-          haml :select
-        end
-      rescue
+      @compounds = PubChemCompound.from_name params[:name]
+      if @compounds.nil?
         haml :not_found
+      elsif @compounds.is_a? Array
+        haml :select
+      else
+        @compound = @compounds
+        haml :compound
       end
     end
 
     get '/cid/:cid/targets/?' do
-      @assays = session[:compound].targets
-      haml :targets, :layout => false
+      @assays = @compound.targets
+      if @assays.empty?
+        "<br><em>No PubChem data</em></br>"
+      else
+        haml :targets, :layout => false
+      end
     end
 
     get '/cid/:cid/nontargets/?' do
-      @assays = session[:compound].non_targets
-      haml :targets, :layout => false
+      @assays = @compound.non_targets
+      if @assays.empty?
+        "<br><em>No PubChem data</em></br>"
+      else
+        haml :targets, :layout => false
+      end
     end
 
     get '/cid/:cid/other_active_assays/?' do
-      @assays = session[:compound].active_assays - session[:compound].targets
-      haml :assays, :layout => false
+      @assays = @compound.active_assays - @compound.targets
+      if @assays.empty?
+        "<br><em>No PubChem data</em></br>"
+      else
+        haml :assays, :layout => false
+      end
     end
 
     get '/cid/:cid/other_inactive_assays/?' do
-      @assays = session[:compound].inactive_assays - session[:compound].non_targets
-      haml :assays, :layout => false
+      @assays = @compound.inactive_assays - @compound.non_targets
+      if @assays.empty?
+        "<br><em>No PubChem data</em></br>"
+      else
+        haml :assays, :layout => false
+      end
     end
 
     get '/cid/:cid/predicted_targets/?' do
-      @assays = session[:compound].predicted_targets
+      @assays = @compound.predicted_targets
+      puts @assays.inspect
       haml :predicted_targets, :layout => false
     end
 
     get '/cid/:cid/predicted_nontargets/?' do
-      @assays = session[:compound].predicted_non_targets
+      @assays = @compound.predicted_non_targets
       haml :predicted_targets, :layout => false
     end
 
     get '/cid/:cid/other_predicted_active_assays/?' do
-      @assays = session[:compound].predicted_active_assays - session[:compound].predicted_targets
+      @assays = @compound.predicted_active_assays - @compound.predicted_targets
       haml :predicted_assays, :layout => false
     end
 
     get '/cid/:cid/other_predicted_inactive_assays/?' do
-      @assays = session[:compound].predicted_inactive_assays - session[:compound].predicted_non_targets
+      @assays = @compound.predicted_inactive_assays - @compound.predicted_non_targets
       haml :predicted_assays, :layout => false
     end
 
@@ -88,23 +97,8 @@ module OpenTox
     end
 
     get '/cid/:cid/cosine/:cid2/?' do
-      session[:compound].cosine(PubChemCompound.new(params[:cid2])).round(3).to_s
-    end
-
-=begin
-    get '/aid/:aid/?' do
-      puts File.join(@@pug_uri, "assay", "aid", params[:aid].to_s, "description", "JSON")
-      json = RestClient.get File.join(@@pug_uri, "assay", "aid", params[:aid].to_s, "description", "JSON")
-      @description = JSON.parse(json)["PC_AssayContainer"][0]["assay"]["descr"]
-      haml :assay_description, :layout => false
-    end
-
-    get '/pubchem_proxy/*' do |path|
-      puts path.inspect
-      puts "http://pubchem.ncbi.nlm.nih.gov/rest/pug/#{path}"
-      RestClientWrapper.get "http://pubchem.ncbi.nlm.nih.gov/rest/pug/#{path}"
+      @compound.cosine(PubChemCompound.new(params[:cid2])).round(3).to_s
     end
-=end
 
     get '/fp/?' do
       @fp = []