Initial GUI

1 files changed, 179 insertions, 18 deletions

diff --git a/application.rb b/application.rb
index 2a77013..a3d46c3 100644
--- a/application.rb
+++ b/application.rb
@@ -1,22 +1,183 @@
-require 'sinatra'
-require "sinatra/reloader" 
-require "haml"
-require 'yaml'
 require "./pubchem.rb"
-also_reload './pubchem.rb'
-
-get '/?' do
-  #@neighbors = OpenTox::PubChemNeighbors.new
-  smiles = "OC(=O)C1=C(C=CC=C1)OC(=O)C"
-  #smiles = "c1cc(CC)ccc1"
-  #smiles = "CC(=O)Nc1ccc(O)cc1"
-  smiles = "C1=CC(=C(C=C1Cl)Cl)OCC(=O)O"
-  #@compound.from_smiles smiles
-  #@neighbors.from_smiles smiles
+require 'rack/session/dalli'
+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
-  File.open("compound.yaml","w+"){|f| f.puts @compound.to_yaml}
-  @compound = YAML.load_file "compound.yaml"
+      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
-  @neighbors = YAML.load_file "search.yaml"
-  haml :index
+
+      def image_uri cid
+        File.join @@pug_uri, "compound", "cid", cid, "PNG"#?record_type=3d&image_size=small"
+      end
+
+    end
+
+    before '/cid/:cid/*' do
+      session[:compound] = PubChemCompound.new params[:cid] unless session[:compound] and session[:compound].cid == params[:cid]
+    end
+
+    get '/?' do
+      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")
+        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
+        #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
+      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
+      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
+      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
+      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
+      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
+      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
+      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
+    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
+    end
+
+    get '/fp/?' do
+      @fp = []
+      YAML.load_file("false_positives.yaml").each do |pred|
+        pred[:fp_targets].each do |gi,t|
+          @fp << {
+            "CID" => pred[:cid],
+            "Target GI" => gi,
+            "p_active" => t[:p][:active].first, 
+            "p_inactive" => t[:p][:inactive].first, 
+            :assays => t[:measured],
+            :neighbors => t[:neighbors]
+          }
+        end
+      end
+      @fp.sort!{|a,b| b["p_active"] <=> a["p_active"]}
+      haml :fp
+    end
+  end
 end