working version without proxy

9 files changed, 123 insertions, 82 deletions

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']}
+