working version with proxy

7 files changed, 93 insertions, 103 deletions

diff --git a/views/compound.haml b/views/compound.haml
index de4cf77..9509ce0 100644
--- a/views/compound.haml
+++ b/views/compound.haml
@@ -1,65 +1,41 @@
-%script{:type => "text/javascript", :src  => "sorttable.js"}
-%table{:class => "sortable"}
-  %tr
-    %th Structure
-    %th Targets (experimental data)
-    %th Other active assays (experimental data)
+:javascript
+  $(document).ready(function() {
+    /*/ prefetch predictions in order to fill cache in background
+    $.ajax({ 
+      url: "/cid/#{@compound.cid}/predicted_targets",
+      cache: true,
+      dataType: "html"
+    });
+    */
+    hide("Measured gene/protein targets",".targets", "/cid/#{@compound.cid}/targets");
+    hide("Other active assays",".active_assays", "/cid/#{@compound.cid}/other_active_assays");
+    hide("Measured gene/protein non-targets",".nontargets", "/cid/#{@compound.cid}/nontargets");
+    hide("Other inactive assays",".inactive_assays", "/cid/#{@compound.cid}/other_inactive_assays");
+    hide("Read across gene/protein targets",".predicted_targets", "/cid/#{@compound.cid}/predicted_targets");
+    hide("Other active read across assays",".predicted_active_assays", "/cid/#{@compound.cid}/other_predicted_active_assays");
+    hide("Read across gene/protein non-targets",".predicted_nontargets", "/cid/#{@compound.cid}/predicted_nontargets");
+    hide("Other inactive read across assays",".predicted_inactive_assays", "/cid/#{@compound.cid}/other_predicted_inactive_assays");
+    hide("Similar compounds",".neighbors", "/cid/#{@compound.cid}/neighbors");
+  });
+
+%table
+  %colgroup
+    %col{:width => "25%"}
+    %col{:width => "37%"}
+    %col{:width => "37%"}
   %tr
     %td{:valign => "top"}
-      %br= session[:compound].name
-      %img{:src => session[:compound].image_uri}
+      %br= @compound.name
+      %img{:src => @compound.image_uri}
     %td{:valign => "top"}
       .targets
-      :javascript
-        display(".targets", "/cid/#{session[:compound].cid}/targets");
-    %td{:valign => "top"}
-      .active_assays
-      :javascript
-        display(".active_assays", "/cid/#{session[:compound].cid}/other_active_assays");
-  %tr
-    %th 
-    %th Targets (predicted)
-    %th Other active assays (predicted)
-  %tr
-    %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"}
+      .active_assays
+      .predicted_active_assays
+      .inactive_assays
       .predicted_inactive_assays
-      :javascript
-        display(".predicted_inactive_assays", "/cid/#{session[:compound].cid}/other_predicted_inactive_assays");
 
-%h2 Read across compounds
 .neighbors
-:javascript
-  display(".neighbors", "/cid/#{session[:compound].cid}/neighbors");
diff --git a/views/layout.haml b/views/layout.haml
index 40c6747..1abb7a8 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -3,6 +3,26 @@
   %head
     %script{:type => "text/javascript", :src  => "jquery-1.8.2.js"}
     :javascript
+      function show(title,element,uri) {
+        $(element).html("<h4>"+title+"</h4>"+"<img src=\"/spinning-wait-icons/wait30trans.gif\" alt=\"Searching PubChem\">");
+        $.ajax({
+          cache: true,
+          url: uri,
+          success: function(data){
+            data = "<h4>"+title+"</h4>"+"<button onclick='hide(\"" + title + "\",\"" + element + "\",\"" + uri + "\");'>Hide</button>" + data;
+            $(element).html(data);
+          },
+          error: function(data,textStatus,message){
+            $(element).html(message);
+          }
+        });
+      }
+
+      function hide(title,element,uri) {
+        data = "<h4>"+title+"</h4>"+"<button onclick='show(\"" + title + "\",\""  + element + "\",\"" + uri + "\");'>Show</button>";
+        $(element).html(data);
+      }
+
       function display(element,uri) {
         $(element).html("<img src=\"/spinning-wait-icons/wait30trans.gif\" alt=\"Searching PubChem\">");
         $.ajax({
@@ -18,7 +38,7 @@
       }
 
   %body
-    %h1 adverse outcome pathways
+    %h1 AOP read across
     %form{:name => "form", :action => '/search', :method => "GET"}
       %fieldset
         %label{:for => 'name'} Compound name:
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 7b9c79d..09dc6cf 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -1,37 +1,33 @@
 %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"}
-        :javascript
-          display("#sim#{compound.cid}", "/cid/#{session[:compound].cid}/cosine/#{compound.cid}");
-      %td{:id => "targets#{compound.cid}", :valign => "top"}
-        :javascript
-          display("#targets#{compound.cid}", "/cid/#{compound.cid}/targets");
-      %td{:id => "assays#{compound.cid}", :valign => "top"}
-        :javascript
-          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");
+  %colgroup
+    %col{:width => "25%"}
+    %col{:width => "37%"}
+    %col{:width => "37%"}
+  - idx = 0
+  - while idx < 10
+    - @compound.neighbors.each do |n|
+      - unless n.assays.empty?
+        %tr
+          %td{:valign => "top"}
+            %br
+              = n.name
+              (
+              = @compound.cosine(n).round(3)
+              )
+            %img{:src => n.image_uri}
+          %td{:valign => "top"}
+            %p{:id => "targets#{n.cid}"}
+              :javascript
+                hide("Measured gene/protein targets","#targets#{n.cid}", "/cid/#{n.cid}/targets");
+            %p{:id => "nontargets#{n.cid}"}
+              :javascript
+                hide("Measured gene/protein non-targets","#nontargets#{n.cid}", "/cid/#{n.cid}/nontargets");
+          %td{:valign => "top"}
+            %p{:id => "assays#{n.cid}"}
+              :javascript
+                hide("Other active assays","#assays#{n.cid}", "/cid/#{n.cid}/other_active_assays");
+            %p{:id => "inactive_assays#{n.cid}"}
+              :javascript
+                hide("Other inactive assays","#inactive_assays#{n.cid}", "/cid/#{n.cid}/other_inactive_assays");
+        
+        - idx += 1
diff --git a/views/nontargets.haml b/views/nontargets.haml
deleted file mode 100644
index 154b5da..0000000
--- a/views/nontargets.haml
+++ /dev/null
@@ -1,3 +0,0 @@
-%pre
-  =# session[:compound].non_targets.to_yaml
-
diff --git a/views/not_found.haml b/views/not_found.haml
index 5903559..6b3485f 100644
--- a/views/not_found.haml
+++ b/views/not_found.haml
@@ -1,2 +1,3 @@
-No compound found that matches name 
-= "\"#{params[:name]}\"."
+Could not find a compound with name 
+= "\"#{params[:name]}\""
+in PubChem.
diff --git a/views/predicted_assays.haml b/views/predicted_assays.haml
index 991c267..299abf4 100644
--- a/views/predicted_assays.haml
+++ b/views/predicted_assays.haml
@@ -1,5 +1,5 @@
 %dl
-  - @assays.sort{|a,b| [b[:p_active],b[:p_inactive]].max <=> [a[:p_active],a[:p_inactive]].max}.each do |assay|
+  - @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
@@ -7,7 +7,7 @@
       %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)
+      = assay["p_active"].to_f.round(3)
     %dd
       p_inactive:
-      = assay[:p_inactive].to_f.round(3)
+      = assay["p_inactive"].to_f.round(3)
diff --git a/views/predicted_targets.haml b/views/predicted_targets.haml
index 523a217..97c68c4 100644
--- a/views/predicted_targets.haml
+++ b/views/predicted_targets.haml
@@ -1,15 +1,15 @@
 %dl
-  - @assays.sort{|a,b| [b[:p_active],b[:p_inactive]].max <=> [a[:p_active],a[:p_inactive]].max}.each do |assay|
+  - @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']}
+      %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)
+      = assay["p_active"].to_f.round(3)
     %dd
       p_inactive:
-      = assay[:p_inactive].to_f.round(3)
+      = assay["p_inactive"].to_f.round(3)