Merge branch 'fileoutput' into feature/hide_elements

Conflicts:
	application.rb
	views/layout.haml
	views/neighbors.haml
	views/style.scss

3 files changed, 97 insertions, 14 deletions

diff --git a/application.rb b/application.rb
index 4cd247f..02b8978 100644
--- a/application.rb
+++ b/application.rb
@@ -12,6 +12,7 @@ class Application < Sinatra::Base
   set :root, File.dirname(__FILE__)
 
   # doc @ http://pubchem.ncbi.nlm.nih.gov/pug_rest/
+  # doc @ http://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html
   PUG_URI = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/"
   SIMILARITY_THRESHOLD = 90
   MAX_NEIGHBORS = 100
@@ -116,6 +117,53 @@ class Application < Sinatra::Base
     end
   end
 
+  def csv_file type
+    case type
+    when "target"
+      out = "\"Target Name\";\"Target GeneID\";\"Assay IDs\"\n"
+      @assays.collect{|a| [a["Target Name"],a["Target GI"]]}.uniq.sort{|a,b| a[0] <=> b[0]}.each do |target|
+        out += "\"#{target.first}\";\"#{target.last}\";\"" + @assays.select{|a| a["Target GI"] == target.last}.collect{|assay| "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=#{assay["AID"]}"}.join(", ") + "\"\n"
+      end
+    when "target_readacross"
+      out = "\"Target Name\";\"Target GeneID\";\"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['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
@@ -127,6 +175,7 @@ class Application < Sinatra::Base
   end
 
   before '/cid/:cid/*' do
+    @accept = request.env['HTTP_ACCEPT']
     @cid = params[:cid] 
   end
 
@@ -156,28 +205,61 @@ 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]
-    @assays and !@assays.empty? ? haml(:targets, :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("target") : "No PubChem data\n"
+    else
+      @assays and !@assays.empty? ? haml(:targets, :layout => false) : "<p><em>No PubChem data</em></p>"
+    end
   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>Insufficient 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]
-    @assays and !@assays.empty? ? haml(:predicted_targets, :layout => false) : "<p><em>Insufficient 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("target_readacross") : "No PubChem data\n"
+    else
+      @assays and !@assays.empty? ? haml(:predicted_targets, :layout => false) : "<p><em>Insuffucient PubChem data for read across predictions.</em></p>"
+    end
   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 280301b..b6b4c0e 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -13,7 +13,8 @@
           url: uri,
           //timeout: 120000;
           success: function(data){
-            data = "<h4>"+title+"</h4>"+"<button onclick='hide(\"" + title + "\",\"" + element + "\",\"" + uri + "\");'>Hide</button>" + data;
+            var slash = new RegExp("/","g");
+            data = "<h4>"+title+"</h4>"+"<button onclick='hide(\"" + title + "\",\"" + element + "\",\"" + uri + "\");'>Hide</button> <a href=\"" + uri + "/" + uri.replace("/cid/", "").replace(slash,'-') + ".csv\"> (csv)</a>" + data;
             $(element).html(data);
           },
           error: function(data,textStatus,message){
@@ -117,4 +118,3 @@
           return false;
         });
       });
-
diff --git a/views/style.scss b/views/style.scss
index 1ec0990..25833e7 100644
--- a/views/style.scss
+++ b/views/style.scss
@@ -39,9 +39,10 @@ h4 {
 
 /* tables */
 th {
-  color: #333;
+  color: #000;
   text-align: left;
-  font-size: 1em;
+  font-size: 1.1em;
+  padding: 8px 0;
 }
 td {
   vertical-align: top;