working version without proxy

13 files changed, 186 insertions, 183 deletions

diff --git a/Gemfile b/Gemfile
index 48f78eb..1dff064 100644
--- a/Gemfile
+++ b/Gemfile
@@ -2,5 +2,7 @@ source :gemcutter
 gemspec
 gem "haml"
 gem "dalli"
+gem "rack-cache"
+gem "rest-client-components"
 gem "opentox-server", :path => "../opentox-server"
 gem "opentox-client", :path => "../opentox-client"
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|
diff --git a/config.ru b/config.ru
index 4050809..76b7b7a 100644
--- a/config.ru
+++ b/config.ru
@@ -1,6 +1,10 @@
 SERVICE = "aop"
 require 'bundler'
 Bundler.require
-timeout = 600
 require './application.rb'
+use Rack::Session::Dalli, :cache => Dalli::Client.new
+#use Rack::Cache,
+#  :verbose => true,
+#  :metastore   => "memcached://127.0.0.1:11211/meta",
+#  :entitystore => "memcached://127.0.0.1:11211/body"
 run OpenTox::Application
diff --git a/pubchem.rb b/pubchem.rb
index a6893fb..ea72553 100644
--- a/pubchem.rb
+++ b/pubchem.rb
@@ -1,6 +1,13 @@
 require '../opentox-client/lib/opentox-client.rb'
 require 'json'
 require 'base64'
+require 'restclient/components'
+require 'rack/cache'
+#RestClient.enable Rack::Cache, :verbose => true#, :allow_reload => true, :allow_revalidate => true
+RestClient.enable Rack::Cache, 
+  :verbose => true,
+  :metastore => 'file:/tmp/cache/meta', 
+  :entitystore => 'file:/tmp/cache/body'
 
 def Math.gauss(x, sigma = 0.3) 
   d = 1.0 - x.to_f
@@ -15,10 +22,11 @@ module OpenTox
     attr_accessor :similarity, :p, :assays
     
     def initialize cid=nil
-      @pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
+      #@pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
+      @pug_uri = "http://localhost:8081/"
       @cid = cid
       @assays = nil
-      @similarity_threshold = 85
+      @similarity_threshold = 90
       @neighbors = nil
       @predicted_assays = nil
       #@predicted_targets = nil
@@ -42,7 +50,7 @@ module OpenTox
       pug_uri = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name"
       compounds = []
       session[:name] = name
-      cid = RestClientWrapper.get(File.join(pug_uri,URI.escape(name),"cids","TXT"))
+      cid = RestClient.get(File.join(pug_uri,URI.escape(name),"cids","TXT"))
       #puts response
       #response.split("\n") do |cid|
         puts cid
@@ -53,6 +61,10 @@ module OpenTox
       compounds
     end
 
+    def name
+      RestClient.get File.join(@pug_uri, "compound", "cid", cid.to_s, "property", "IUPACName","TXT").chomp
+    end
+
     def neighbors
       unless @neighbors
         @neighbors = []
@@ -63,11 +75,11 @@ module OpenTox
           result = pubchem_search File.join(@pug_uri, "compound", "listkey", listkey, "cids", "JSON")
           #result = pubchem_search File.join(@pug_uri, "compound", "listkey", listkey, "assaysummary", "JSON")
         end
-        puts "Neighbor CIDs received"
+        puts "#{result["IdentifierList"]["CID"].size} Neighbor CIDs received"
         result["IdentifierList"]["CID"].each do |cid|
           unless cid.to_s == @cid.to_s
             c = PubChemCompound.new cid.to_s
-            @neighbors << c if c.assays #and !(c.targets + c.non_targets).empty?
+            @neighbors << c if c.assays and !c.assays.empty?
           end
         end if result and result["IdentifierList"]
 =begin
@@ -122,7 +134,7 @@ module OpenTox
         neighbors.collect{|n| n.assays.collect{|a| a["AID"]}}.flatten.compact.uniq.each do |aid|
           predicted_assay = {"AID" => aid}
           neighbors.each do |neighbor|
-            if similarity(neighbor) > 0.5 # avoid downweighting
+            if similarity(neighbor) and similarity(neighbor) > 0.5 # avoid downweighting
               search = neighbor.assays.select{|a| a["AID"] == aid}
               search.each do |assay|
                 predicted_assay["Target GI"] ||= assay["Target GI"]
@@ -168,11 +180,11 @@ module OpenTox
     end
 
     def predicted_targets
-      predicted_active_assays.select{|a| a[:target_gi]} if predicted_assays
+      predicted_active_assays.select{|a| a["Target GI"]} if predicted_assays
     end
 
     def predicted_non_targets
-      inactive_assays.select{|a| a[:target_gi]} if predicted_assays
+      predicted_inactive_assays.select{|a| a["Target GI"]} if predicted_assays
     end
 
     def to_smiles
diff --git a/views/assays.haml b/views/assays.haml
index e995842..510234d 100644
--- a/views/assays.haml
+++ b/views/assays.haml
@@ -1,6 +1,7 @@
-%ul
-  - @assays.each do |assay|
-    %li
-      %a{:href => "/aid/#{assay["AID"]}"} #{assay['Assay Name']}
-      AID:
-      = assay["AID"]
+%dl
+  - @assays.sort{|a,b| a["Assay Name"] <=> b["Assay Name"]}.each do |assay|
+    %dt
+      %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['Assay Name']}
+    %dd
+      Assay ID:
+      %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['AID']}
diff --git a/views/compound.haml b/views/compound.haml
index 7614142..de4cf77 100644
--- a/views/compound.haml
+++ b/views/compound.haml
@@ -1,46 +1,65 @@
-:javascript
-  $(document).ready(function() {
-    display(".targets", "/cid/#{session[:compound].cid}/targets");
-    //display(".nontargets", "/cid/#{session[:compound].cid}/targets");
-    display(".active_assays", "/cid/#{session[:compound].cid}/other_active_assays");
-    //display(".inactive_assays", "/cid/#{session[:compound].cid}/other_active_assays");
-    display(".predicted_targets", "/cid/#{session[:compound].cid}/predicted_targets");
-    display(".predicted_active_assays", "/cid/#{session[:compound].cid}/other_predicted_active_assays");
-    display(".neighbors", "/cid/#{session[:compound].cid}/neighbors");
-  });
-
 %script{:type => "text/javascript", :src  => "sorttable.js"}
 %table{:class => "sortable"}
   %tr
     %th Structure
-    %th 
     %th Targets (experimental data)
-    %th Other assays (experimental data)
+    %th Other active assays (experimental data)
   %tr
     %td{:valign => "top"}
+      %br= session[:compound].name
       %img{:src => session[:compound].image_uri}
-    %td
     %td{:valign => "top"}
       .targets
-      -# %h2 Non-Targets
-        .nontargets
+      :javascript
+        display(".targets", "/cid/#{session[:compound].cid}/targets");
     %td{:valign => "top"}
       .active_assays
-      -# %h2 Inactive assays
-        .inactive_assays
+      :javascript
+        display(".active_assays", "/cid/#{session[:compound].cid}/other_active_assays");
   %tr
     %th 
-    %th 
     %th Targets (predicted)
-    %th Other assays (predicted)
+    %th Other active assays (predicted)
   %tr
     %td
-    %td
     %td{:valign => "top"}
       .predicted_targets
+      :javascript
+        display(".predicted_targets", "/cid/#{session[:compound].cid}/predicted_targets");
     %td{:valign => "top"}
       .predicted_active_assays
+      :javascript
+        display(".predicted_active_assays", "/cid/#{session[:compound].cid}/other_predicted_active_assays");
+  %tr
+    %th 
+    %th Non-targets (experimental data)
+    %th Other inactive assays (experimental data)
+  %tr
+    %td
+    %td{:valign => "top"}
+      .nontargets
+      :javascript
+        display(".nontargets", "/cid/#{session[:compound].cid}/nontargets");
+    %td{:valign => "top"}
+      .inactive_assays
+      :javascript
+        display(".inactive_assays", "/cid/#{session[:compound].cid}/other_inactive_assays");
+  %tr
+    %th 
+    %th Non-targets (predicted)
+    %th Other inactive assays (predicted)
+  %tr
+    %td
+    %td{:valign => "top"}
+      .predicted_nontargets
+      :javascript
+        display(".predicted_nontargets", "/cid/#{session[:compound].cid}/predicted_nontargets");
+    %td{:valign => "top"}
+      .predicted_inactive_assays
+      :javascript
+        display(".predicted_inactive_assays", "/cid/#{session[:compound].cid}/other_predicted_inactive_assays");
 
-%h2 Neighbors
+%h2 Read across compounds
 .neighbors
-
+:javascript
+  display(".neighbors", "/cid/#{session[:compound].cid}/neighbors");
diff --git a/views/layout.haml b/views/layout.haml
index 8641692..40c6747 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -6,6 +6,7 @@
       function display(element,uri) {
         $(element).html("<img src=\"/spinning-wait-icons/wait30trans.gif\" alt=\"Searching PubChem\">");
         $.ajax({
+          cache: true,
           url: uri,
           success: function(data){
             $(element).html(data);
@@ -20,7 +21,7 @@
     %h1 adverse outcome pathways
     %form{:name => "form", :action => '/search', :method => "GET"}
       %fieldset
-        %label{:for => 'identifier'} Compound name:
-        %input{:type => 'text', :name => 'name', :id => 'name', :size => '60'}
-        %input{ :type => "submit", :value => "Predict" }
+        %label{:for => 'name'} Compound name:
+        %input{:type => 'text', :name => 'name', :id => 'name'}
+        %input{ :type => "submit", :value => "Search" }
     = yield
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 54905ce..7b9c79d 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -1,43 +1,37 @@
-%script{:type => "text/javascript", :src  => "sorttable.js"}
-%table{:class => "sortable"}
+%table
   - session[:compound].neighbors[0..10].each do |compound|
     %tr
+      %th Structure
+      %th Similarity
+      %th Targets (experimental data)
+      %th Other active assays (experimental data)
+
+    %tr
       %td{:valign => "top"}
+        %br= compound.name
         %img{:src => compound.image_uri}
       %td{:id => "sim#{compound.cid}", :valign => "top"}
-        %img{:src => "/spinning-wait-icons/wait30trans.gif"}
         :javascript
-          $.ajax({
-            url: "/cid/#{session[:compound].cid}/cosine/#{compound.cid}",
-            success: function(data){
-              $("#sim#{compound.cid}").html(data);
-            },
-            error: function(data,textStatus,message){
-              $("#sim#{compound.cid}").html(message);
-            }
-          });
+          display("#sim#{compound.cid}", "/cid/#{session[:compound].cid}/cosine/#{compound.cid}");
       %td{:id => "targets#{compound.cid}", :valign => "top"}
-        %img{:src => "/spinning-wait-icons/wait30trans.gif"}
         :javascript
-          $.ajax({
-            url: "/cid/#{compound.cid}/targets",
-            success: function(data){
-              $("#targets#{compound.cid}").html(data);
-            },
-            error: function(data,textStatus,message){
-              $("#targets#{compound.cid}").html(message);
-            }
-          });
+          display("#targets#{compound.cid}", "/cid/#{compound.cid}/targets");
       %td{:id => "assays#{compound.cid}", :valign => "top"}
-        %img{:src => "/spinning-wait-icons/wait30trans.gif"}
         :javascript
-          $.ajax({
-            url: "/cid/#{compound.cid}/other_active_assays",
-            success: function(data){
-              $("#assays#{compound.cid}").html(data);
-            },
-            error: function(data,textStatus,message){
-              $("#assays#{compound.cid}").html(message);
-            }
-          });
+          display("#assays#{compound.cid}", "/cid/#{compound.cid}/other_active_assays");
+    
+    %tr
+      %th 
+      %th 
+      %th Non-targets (experimental data)
+      %th Other inactive assays (experimental data)
+
+    %tr
+      %td
       %td
+      %td{:id => "targets#{compound.cid}", :valign => "top"}
+        :javascript
+          display("#targets#{compound.cid}", "/cid/#{compound.cid}/nontargets");
+      %td{:id => "assays#{compound.cid}", :valign => "top"}
+        :javascript
+          display("#assays#{compound.cid}", "/cid/#{compound.cid}/other_inactive_assays");
diff --git a/views/nontargets.haml b/views/nontargets.haml
new file mode 100644
index 0000000..154b5da
--- /dev/null
+++ b/views/nontargets.haml
@@ -0,0 +1,3 @@
+%pre
+  =# session[:compound].non_targets.to_yaml
+
diff --git a/views/not_found.haml b/views/not_found.haml
new file mode 100644
index 0000000..5903559
--- /dev/null
+++ b/views/not_found.haml
@@ -0,0 +1,2 @@
+No compound found that matches name 
+= "\"#{params[:name]}\"."
diff --git a/views/predicted_assays.haml b/views/predicted_assays.haml
index e995842..991c267 100644
--- a/views/predicted_assays.haml
+++ b/views/predicted_assays.haml
@@ -1,6 +1,13 @@
-%ul
-  - @assays.each do |assay|
-    %li
-      %a{:href => "/aid/#{assay["AID"]}"} #{assay['Assay Name']}
-      AID:
-      = assay["AID"]
+%dl
+  - @assays.sort{|a,b| [b[:p_active],b[:p_inactive]].max <=> [a[:p_active],a[:p_inactive]].max}.each do |assay|
+    %dt
+      %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['Assay Name']}
+    %dd
+      Assay ID:
+      %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['AID']}
+    %dd
+      p_active:
+      = assay[:p_active].to_f.round(3)
+    %dd
+      p_inactive:
+      = assay[:p_inactive].to_f.round(3)
diff --git a/views/predicted_targets.haml b/views/predicted_targets.haml
index 1a172ff..523a217 100644
--- a/views/predicted_targets.haml
+++ b/views/predicted_targets.haml
@@ -1,6 +1,15 @@
-%ul
-  - @assays.each do |assay|
-    %li
-      %a{:href => "/aid/#{assay["AID"]}"} #{assay['Target Name']}
-      Target GI:
-      = assay['Target GI']
+%dl
+  - @assays.sort{|a,b| [b[:p_active],b[:p_inactive]].max <=> [a[:p_active],a[:p_inactive]].max}.each do |assay|
+    %dt= assay["Target Name"]
+    %dd
+      Target GeneID:
+      = assay["Target GI"]
+    %dd
+      Assay ID:
+      %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['AID']}
+    %dd
+      p_active:
+      = assay[:p_active].to_f.round(3)
+    %dd
+      p_inactive:
+      = assay[:p_inactive].to_f.round(3)
diff --git a/views/targets.haml b/views/targets.haml
index 1a172ff..9622abd 100644
--- a/views/targets.haml
+++ b/views/targets.haml
@@ -1,6 +1,11 @@
-%ul
-  - @assays.each do |assay|
-    %li
-      %a{:href => "/aid/#{assay["AID"]}"} #{assay['Target Name']}
-      Target GI:
-      = assay['Target GI']
+%dl
+  - @assays.collect{|a| [a["Target Name"],a["Target GI"]]}.uniq.sort{|a,b| a[0] <=> b[0]}.each do |target|
+    %dt= target.first
+    %dd
+      Target GeneID:
+      = target.last
+    %dd
+      Assay IDs:
+      - @assays.select{|a| a["Target GI"] == target.last}.each do |assay|
+        %a{:href => "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"} #{assay['AID']}
+