working version without proxy

1 files changed, 36 insertions, 92 deletions

diff --git a/application.rb b/application.rb
index a3d46c3..68bb8d2 100644
--- a/application.rb
+++ b/application.rb
@@ -1,70 +1,36 @@
 require "./pubchem.rb"
 require 'rack/session/dalli'
+require "rack/cache"
 module OpenTox
   class Application < Service
     set :static, true
     set :root, File.dirname(__FILE__)
     also_reload './pubchem.rb'
-    #enable :sessions
-    use Rack::Session::Dalli, :cache => Dalli::Client.new
 
     @@pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
 
-    helpers do
-
-=begin
-      def pubchem_search url
-        attempts = 0
-        result = nil
-        begin
-          attempts += 1
-          json = RestClient.get url, :timeout => 90000000
-          result = JSON.parse json
-          while result["Waiting"] do
-            sleep 2
-            listkey = result["Waiting"]["ListKey"]
-            result = pubchem_search File.join(@pug_uri, "compound", "listkey", listkey, "cids", "JSON")
-          end
-        rescue
-          if $!.message =~ /Timeout/i and attempts < 4
-            sleep 2
-            retry
-          elsif $!.message =~ /Timeout/i and attempts >= 4
-            File.open("timeouts","a+"){|f| f.puts url}
-            puts url
-            puts $!.message
-          elsif $!.message.match /404/
-            #not_found_error #TODO
-          else
-            puts url
-            puts $!.message
-          end
-        end
-      end
-=end
-
-      def image_uri cid
-        File.join @@pug_uri, "compound", "cid", cid, "PNG"#?record_type=3d&image_size=small"
-      end
-
+    before do
+      #cache_control :public, :max_age => 3600
     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]
     end
 
     get '/?' do
+      #cache_control :public, :no_cache
       haml :index
     end
 
     get '/cid/:cid/?' do
-      session[:compound] = PubChemCompound.new params[:cid]
       haml :compound
     end
 
     get '/search/?' do
-      #begin
-        cids = RestClientWrapper.get(File.join(@@pug_uri,"compound","name",URI.escape(params[:name]),"cids","TXT")).split("\n")
+      #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
@@ -72,96 +38,74 @@ module OpenTox
           @compounds = cids.collect{|cid| PubChemCompound.new cid }
           haml :select
         end
-      #rescue
-        #haml :not_found
-      #end
+      rescue
+        haml :not_found
+      end
     end
 
     get '/cid/:cid/targets/?' do
-      if params[:cid] == session[:compound].cid
-        @assays = session[:compound].targets
-      else
-        @assays = PubChemCompound.new(params[:cid]).targets
-      end
+      @assays = session[:compound].targets
       haml :targets, :layout => false
     end
 
     get '/cid/:cid/nontargets/?' do
-      if params[:cid] == session[:compound].cid
-        @assays = session[:compound].non_targets
-      else
-        @assays = PubChemCompound.new(params[:cid]).non_targets
-      end
+      @assays = session[:compound].non_targets
       haml :targets, :layout => false
     end
 
     get '/cid/:cid/other_active_assays/?' do
-      if params[:cid] == session[:compound].cid
-        @assays = session[:compound].active_assays - session[:compound].targets
-      else
-        compound = PubChemCompound.new(params[:cid])
-        @assays = compound.active_assays - compound.targets
-      end
+      @assays = session[:compound].active_assays - session[:compound].targets
       haml :assays, :layout => false
     end
 
     get '/cid/:cid/other_inactive_assays/?' do
-      if params[:cid] == session[:compound].cid
-        @assays = session[:compound].inactive_assays - session[:compound].non_targets
-      else
-        compound = PubChemCompound.new(params[:cid])
-        @assays = compound.inactive_assays - compound.non_targets
-      end
+      @assays = session[:compound].inactive_assays - session[:compound].non_targets
       haml :assays, :layout => false
     end
 
     get '/cid/:cid/predicted_targets/?' do
-      if params[:cid] == session[:compound].cid
-        @assays = session[:compound].predicted_targets
-      else
-        @assays = PubChemCompound.new(params[:cid]).predicted_targets
-      end
+      @assays = session[:compound].predicted_targets
       haml :predicted_targets, :layout => false
     end
 
     get '/cid/:cid/predicted_nontargets/?' do
-      if params[:cid] == session[:compound].cid
-        @assays = session[:compound].predicted_non_targets
-      else
-        @assays = PubChemCompound.new(params[:cid]).predicted_non_targets
-      end
+      @assays = session[:compound].predicted_non_targets
       haml :predicted_targets, :layout => false
     end
 
     get '/cid/:cid/other_predicted_active_assays/?' do
-      if params[:cid] == session[:compound].cid
-        @assays = session[:compound].predicted_active_assays - session[:compound].predicted_targets
-      else
-        compound = PubChemCompound.new(params[:cid])
-        @assays = compound.predicted_active_assays - compound.predicted_targets
-      end
+      @assays = session[:compound].predicted_active_assays - session[:compound].predicted_targets
       haml :predicted_assays, :layout => false
     end
 
     get '/cid/:cid/other_predicted_inactive_assays/?' do
-      if params[:cid] == session[:compound].cid
-        @assays = session[:compound].predicted_inactive_assays - session[:compound].predicted_non_targets
-      else
-        compound = PubChemCompound.new(params[:cid])
-        @assays = compound.predicted_inactive_assays - compound.predicted_non_targets
-      end
-      haml :assays, :layout => false
+      @assays = session[:compound].predicted_inactive_assays - session[:compound].predicted_non_targets
+      haml :predicted_assays, :layout => false
     end
 
     get '/cid/:cid/neighbors/?' do
       haml :neighbors, :layout => false
     end
 
-
     get '/cid/:cid/cosine/:cid2/?' do
-      session[:compound].cosine(PubChemCompound.new(params[:cid2])).to_s
+      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}"
+    end
+=end
+
     get '/fp/?' do
       @fp = []
       YAML.load_file("false_positives.yaml").each do |pred|