From 6d6fdf889eace978aaacbde1335264c9fccaa874 Mon Sep 17 00:00:00 2001
From: rautenberg <rautenberg@in-silico.ch>
Date: Mon, 21 Oct 2013 11:00:04 +0200
Subject: before @accept

---
 application.rb | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/application.rb b/application.rb
index f742442..53fd2f7 100644
--- a/application.rb
+++ b/application.rb
@@ -116,6 +116,11 @@ class Application < Sinatra::Base
     end
   end
 
+  before do
+    @accept = request.env['HTTP_ACCEPT']
+    response['Content-Type'] = @accept
+  end
+
   before '/pug/*' do
     content_type 'application/json'
     @result = CACHE.get request.path
-- 
cgit v1.2.3


From 1a779e4fab4f42f27d867fcda24bf207cc2ece8a Mon Sep 17 00:00:00 2001
From: rautenberg <rautenberg@in-silico.ch>
Date: Wed, 23 Oct 2013 00:18:26 +0200
Subject: add basic csv download posibilities

---
 application.rb    | 47 ++++++++++++++++++++++++++++++++++++++++++-----
 views/layout.haml |  2 +-
 2 files changed, 43 insertions(+), 6 deletions(-)

diff --git a/application.rb b/application.rb
index 53fd2f7..ddc4aa4 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
@@ -116,9 +117,20 @@ class Application < Sinatra::Base
     end
   end
 
-  before do
-    @accept = request.env['HTTP_ACCEPT']
-    response['Content-Type'] = @accept
+  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
+    end
+    out
   end
 
   before '/pug/*' do
@@ -132,6 +144,7 @@ class Application < Sinatra::Base
   end
 
   before '/cid/:cid/*' do
+    @accept = request.env['HTTP_ACCEPT']
     @cid = params[:cid] 
   end
 
@@ -163,7 +176,19 @@ class Application < Sinatra::Base
 
   get '/cid/:cid/targets/:outcome' do
     @assays = targets params[:cid], params[:outcome]
-    @assays and !@assays.empty? ? haml(:targets, :layout => false) : "<p><em>No PubChem data</em></p>" 
+    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"
+    else
+      @assays and !@assays.empty? ? haml(:targets, :layout => false) : "<p><em>No PubChem data</em></p>"
+    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
@@ -178,7 +203,19 @@ class Application < Sinatra::Base
 
   get '/cid/:cid/prediction/targets/:outcome' do
     @assays = predicted_targets params[:cid], params[:outcome]
-    @assays and !@assays.empty? ? haml(:predicted_targets, :layout => false) : "<p><em>Insuffucient PubChem data for read across predictions.</em></p>"
+    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"
+    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/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
diff --git a/views/layout.haml b/views/layout.haml
index 827baaf..1e1c7d3 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -14,7 +14,7 @@
           url: uri,
           //timeout: 120000;
           success: function(data){
-            data = "<h4>"+title+"</h4>"+"<button onclick='hide(\"" + title + "\",\"" + element + "\",\"" + uri + "\");'>Hide</button>" + data;
+            data = "<h4>"+title+"</h4>"+"<button onclick='hide(\"" + title + "\",\"" + element + "\",\"" + uri + "\");'>Hide</button> <a href=\"" + uri + "/" + uri.replace("/cid/", "").replace("/",'-','g') + ".csv\"> (csv)</a>" + data;
             $(element).html(data);
           },
           error: function(data,textStatus,message){
-- 
cgit v1.2.3


From 773c75117fecdb6c328ce7ad8c8ce9d89e552f03 Mon Sep 17 00:00:00 2001
From: rautenberg <rautenberg@in-silico.ch>
Date: Wed, 23 Oct 2013 11:26:33 +0200
Subject: extend csv file feature, add ist link

---
 application.rb    | 80 +++++++++++++++++++++++++++++++++++++++++--------------
 views/layout.haml |  3 +++
 views/style.scss  | 10 +++++++
 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
-- 
cgit v1.2.3


From 9095a48b0e22f51ece2f4e9539e41310ff544052 Mon Sep 17 00:00:00 2001
From: rautenberg <rautenberg@in-silico.ch>
Date: Wed, 23 Oct 2013 12:27:50 +0200
Subject: IE js replace fix

---
 views/layout.haml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/views/layout.haml b/views/layout.haml
index 976d172..5160c31 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -14,7 +14,8 @@
           url: uri,
           //timeout: 120000;
           success: function(data){
-            data = "<h4>"+title+"</h4>"+"<button onclick='hide(\"" + title + "\",\"" + element + "\",\"" + uri + "\");'>Hide</button> <a href=\"" + uri + "/" + uri.replace("/cid/", "").replace("/",'-','g') + ".csv\"> (csv)</a>" + 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){
-- 
cgit v1.2.3


From f7c3b817e5de6ce3388caee15d1a4adc12b81334 Mon Sep 17 00:00:00 2001
From: rautenberg <rautenberg@in-silico.ch>
Date: Mon, 28 Oct 2013 11:38:33 +0100
Subject: minor style change

---
 views/style.scss | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/views/style.scss b/views/style.scss
index 01e3aa6..225bee8 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;
@@ -111,4 +112,12 @@ img.compound {
   text-decoration: none;
   color: #000;
   &:hover { color: #900; }
+}
+.tooltip {
+  background-color: #fff;
+  border: 2px solid #ccc;
+  font-size: 0.5em;
+  padding: 1em;
+  display: none;
+  z-index: 50;
 }
\ No newline at end of file
-- 
cgit v1.2.3


From ecae07354c9a6b7f13fdf70ef832ccafc9c64d05 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 17 Feb 2014 11:29:47 +0100
Subject: ensure correct loop end

---
 views/neighbors.haml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/views/neighbors.haml b/views/neighbors.haml
index c7a181a..5563392 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -31,4 +31,4 @@
               :javascript
                 hide("Other inactive assays","#inactive_assays#{n}", "/cid/#{n}/assays/inactive");
         
-        - idx += 1
+      - idx += 1
-- 
cgit v1.2.3