extend csv file feature, add ist link

3 files changed, 73 insertions, 20 deletions

diff --git a/application.rb b/application.rb
index ddc4aa4..02b8978 100644
--- a/application.rb
+++ b/application.rb
@@ -129,10 +129,41 @@ class Application < Sinatra::Base
       @assays.sort{|a,b| [b["p_active"],b["p_inactive"]].max <=> [a["p_active"],a["p_inactive"]].max}.each do |assay|
         out += "\"#{assay['Target Name']}\";\"#{assay['Target GI']}\";\"http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay['AID']}\";\"#{assay['p_active'].to_f.round(3)}\";\"#{assay['p_inactive'].to_f.round(3)}\"\n"
       end
+    when "assays"
+      out = "\"Assay Name\";\"Assay ID\"\n"
+      @assays.sort{|a,b| a["Assay Name"] <=> b["Assay Name"]}.each do |assay|
+        out += "\"#{assay['Assay Name']}\";\"http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay['AID']}\"\n"
+      end
+    when "predicted_assays"
+      out = "\"Assay Name\";\"Assay ID\";\"p_active\";\"p_inactive\"\n"
+      @assays.sort{|a,b| [b["p_active"],b["p_inactive"]].max <=> [a["p_active"],a["p_inactive"]].max}.each do |assay|
+        out += "\"#{assay['Assay Name']}\";\"http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay['AID']}\";\"#{assay["p_active"].to_f.round(3)}\";\"#{assay["p_inactive"].to_f.round(3)}\"\n"
+      end
+    when "neighbors"
+      out = "\"Compound Name\";\"Similarity\"\n"
+      idx = 0
+      while idx < 10
+        neighbors(@cid).each do |n|
+          unless assays(n,"active").empty? and assays(n,"inactive").empty?
+            out += "\"#{name n}\";\"#{similarity(@cid,n).round(3)}\"\n"
+            idx += 1
+          end
+        end
+      end
     end
     out
   end
 
+  def set_accept
+    case File.extname(params[:file])
+    when ".csv"
+      @accept = "text/csv"
+    when ".json"
+      @accept = "application/json"
+    end
+    response['Content-Type'] = @accept
+  end
+
   before '/pug/*' do
     content_type 'application/json'
     @result = CACHE.get request.path
@@ -174,10 +205,10 @@ class Application < Sinatra::Base
     end
   end
 
-  get '/cid/:cid/targets/:outcome' do
+  get '/cid/:cid/targets/:outcome/?:file?' do
     @assays = targets params[:cid], params[:outcome]
+    set_accept if params[:file]
     if @accept == "application/json"
-      content_type = @accept
       @assays and !@assays.empty? ? JSON.pretty_generate(@assays) : "No PubChem data\n"
     elsif @accept == "text/csv"
       @assays and !@assays.empty? ? csv_file("target") : "No PubChem data\n"
@@ -186,25 +217,34 @@ class Application < Sinatra::Base
     end
   end
 
-  get '/cid/:cid/targets/:outcome/:file' do
-    response['Content-Type'] = "text/csv"
-    RestClient.get "#{request.host_with_port}/cid/#{params[:cid]}/targets/#{params[:outcome]}",{:accept => "text/csv"}
-  end
-
-  get '/cid/:cid/assays/:outcome' do
+  get '/cid/:cid/assays/:outcome/?:file?' do
     @assays = assays(params[:cid], params[:outcome]) - targets(params[:cid], params[:outcome])
-    @assays and !@assays.empty? ? haml(:assays, :layout => false) : "<p><em>No PubChem data</em></p>"
+    set_accept if params[:file]
+    if @accept == "application/json"
+      @assays and !@assays.empty? ? JSON.pretty_generate(@assays) : "No PubChem data\n"
+    elsif @accept == "text/csv"
+      @assays and !@assays.empty? ? csv_file("assays") : "No PubChem data\n"
+    else
+      @assays and !@assays.empty? ? haml(:assays, :layout => false) : "<p><em>No PubChem data</em></p>"
+    end
   end
 
-  get '/cid/:cid/prediction/assays/:outcome' do
+  get '/cid/:cid/prediction/assays/:outcome/?:file?' do
     @assays = predicted_assays(params[:cid], params[:outcome]) - predicted_targets(params[:cid], params[:outcome])
-    @assays and !@assays.empty? ? haml(:predicted_assays, :layout => false) : "<p><em>Insuffucient PubChem data for read across predictions.</em></p>"
+    set_accept if params[:file]
+    if @accept == "application/json"
+      @assays and !@assays.empty? ? JSON.pretty_generate(@assays) : "No PubChem data\n"
+    elsif @accept == "text/csv"
+      @assays and !@assays.empty? ? csv_file("predicted_assays") : "No PubChem data\n"
+    else
+      @assays and !@assays.empty? ? haml(:predicted_assays, :layout => false) : "<p><em>Insuffucient PubChem data for read across predictions.</em></p>"
+    end
   end
 
-  get '/cid/:cid/prediction/targets/:outcome' do
+  get '/cid/:cid/prediction/targets/:outcome/?:file?' do
     @assays = predicted_targets params[:cid], params[:outcome]
+    set_accept if params[:file]
     if @accept == "application/json"
-      content_type = @accept
       @assays and !@assays.empty? ? JSON.pretty_generate(@assays) : "No PubChem data\n"
     elsif @accept == "text/csv"
       @assays and !@assays.empty? ? csv_file("target_readacross") : "No PubChem data\n"
@@ -213,13 +253,13 @@ class Application < Sinatra::Base
     end
   end
 
-  get '/cid/:cid/prediction/targets/:outcome/:file' do
-    response['Content-Type'] = "text/csv"
-    RestClient.get "#{request.host_with_port}/cid/#{params[:cid]}/prediction/targets/#{params[:outcome]}",{:accept => "text/csv"}
-  end
-
-  get '/cid/:cid/neighbors/?' do
-    haml :neighbors, :layout => false
+  get '/cid/:cid/neighbors/?:file?' do
+    set_accept if params[:file]
+    if @accept == "text/csv"
+      csv_file("neighbors")
+    else
+      haml :neighbors, :layout => false
+    end
   end
 
   get '/pug/cid/:cid/name' do
diff --git a/views/layout.haml b/views/layout.haml
index 1e1c7d3..976d172 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -52,3 +52,6 @@
         %input{ :type => "submit", :value => "Search" }
     %em This is an experimental version. Loading data from PubChem can be slow. Please use the "Back" button and retry the offending operation if you have timeout problems.
     = yield
+
+    .footer
+      %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2013
\ No newline at end of file
diff --git a/views/style.scss b/views/style.scss
index 77f2f5c..01e3aa6 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -101,4 +101,14 @@ img.compound {
     color: $formborder;
     radius: 4px;
   }
+}
+.footer {
+  margin: 200px 0px 20px 4px;
+  width: 99%;
+  text-align: right;
+}
+.footer a {
+  text-decoration: none;
+  color: #000;
+  &:hover { color: #900; }
 }
\ No newline at end of file