Initial GUI

10 files changed, 188 insertions, 27 deletions

diff --git a/views/assays.haml b/views/assays.haml
new file mode 100644
index 0000000..e995842
--- /dev/null
+++ b/views/assays.haml
@@ -0,0 +1,6 @@
+%ul
+  - @assays.each do |assay|
+    %li
+      %a{:href => "/aid/#{assay["AID"]}"} #{assay['Assay Name']}
+      AID:
+      = assay["AID"]
diff --git a/views/compound.haml b/views/compound.haml
new file mode 100644
index 0000000..7614142
--- /dev/null
+++ b/views/compound.haml
@@ -0,0 +1,46 @@
+: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)
+  %tr
+    %td{:valign => "top"}
+      %img{:src => session[:compound].image_uri}
+    %td
+    %td{:valign => "top"}
+      .targets
+      -# %h2 Non-Targets
+        .nontargets
+    %td{:valign => "top"}
+      .active_assays
+      -# %h2 Inactive assays
+        .inactive_assays
+  %tr
+    %th 
+    %th 
+    %th Targets (predicted)
+    %th Other assays (predicted)
+  %tr
+    %td
+    %td
+    %td{:valign => "top"}
+      .predicted_targets
+    %td{:valign => "top"}
+      .predicted_active_assays
+
+%h2 Neighbors
+.neighbors
+
diff --git a/views/fp.haml b/views/fp.haml
new file mode 100644
index 0000000..4bffba3
--- /dev/null
+++ b/views/fp.haml
@@ -0,0 +1,41 @@
+!!! 5
+%style{:type => "text/css" }
+  //dt { float: left; clear: left; width: 100px; text-align: right; font-weight: bold; color: green; }
+  //dt {  float: left; clear: left; text-align: left; font-weight: bold; color: green; }
+  table { border-top: 2px black }
+  dl {text-align:left;}
+  dt { display: inline; text-align: left; font-weight: bold; color: green; }
+  dt:after { content: ": "; }
+  dd {  display: inline; text-align: left; margin:0 }
+  dd:after { content: '\A'; white-space: pre; }
+- @fp.each do |p|
+  %table{:class => "sortable"}
+    %tr
+      %th
+        %img{:src => "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/#{p["CID"]}/PNG"}
+      %th
+        %dl
+          - [ "CID", "Target GI", "p_active", "p_inactive" ].each do |k|
+            %dt= k
+            %dd= p[k]
+      - p[:assays].each do |a|
+        %th
+          %dl
+            - a.each do |k,v|
+              %dt= k
+              %dd= v
+      - p[:neighbors].each do |n|
+        %tr
+          %td
+            %img{:src => "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/#{n[:cid]}/PNG"}
+          %td
+            %dl
+              - ["CID", "Similarity"].each do |k|
+                %dt= k
+                %dd= n[k.downcase.to_sym]
+          - n[:assays].each do |a|
+            %td
+              %dl
+                - a.each do |k,v|
+                  %dt= k
+                  %dd= v
diff --git a/views/index.haml b/views/index.haml
index b75a9ab..e69de29 100644
--- a/views/index.haml
+++ b/views/index.haml
@@ -1,27 +0,0 @@
-!!! 5
-%script{:type => "text/javascript", :src  => "sorttable.js"}
-%table{:class => "sortable"}
-  %tr
-    %th
-      = @neighbors.query.to_name
-      %br
-        %img{:src => @neighbors.query.to_image_uri}
-    %th Structure
-    %th Properties
-    %th Targets
-    %th Assays
-  - @neighbors.neighbors.each do |neighbor|
-    - sim = neighbor.structure_similarity @neighbors.query
-    %tr{:sorttable_customkey => sim}
-      %td
-        = neighbor.to_name
-        %br
-          %img{:src => neighbor.to_image_uri}
-      %td
-        = sim
-      %td
-        = neighbor.property_similarity @neighbors.query
-      %td
-        = neighbor.target_similarity @neighbors.query
-      %td
-        = neighbor.assay_similarity @neighbors.query
diff --git a/views/layout.haml b/views/layout.haml
new file mode 100644
index 0000000..8641692
--- /dev/null
+++ b/views/layout.haml
@@ -0,0 +1,26 @@
+!!! 5
+%html
+  %head
+    %script{:type => "text/javascript", :src  => "jquery-1.8.2.js"}
+    :javascript
+      function display(element,uri) {
+        $(element).html("<img src=\"/spinning-wait-icons/wait30trans.gif\" alt=\"Searching PubChem\">");
+        $.ajax({
+          url: uri,
+          success: function(data){
+            $(element).html(data);
+          },
+          error: function(data,textStatus,message){
+            $(element).html(message);
+          }
+        });
+      }
+
+  %body
+    %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" }
+    = yield
diff --git a/views/neighbors.haml b/views/neighbors.haml
new file mode 100644
index 0000000..54905ce
--- /dev/null
+++ b/views/neighbors.haml
@@ -0,0 +1,43 @@
+%script{:type => "text/javascript", :src  => "sorttable.js"}
+%table{:class => "sortable"}
+  - session[:compound].neighbors[0..10].each do |compound|
+    %tr
+      %td{:valign => "top"}
+        %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);
+            }
+          });
+      %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);
+            }
+          });
+      %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);
+            }
+          });
+      %td
diff --git a/views/predicted_assays.haml b/views/predicted_assays.haml
new file mode 100644
index 0000000..e995842
--- /dev/null
+++ b/views/predicted_assays.haml
@@ -0,0 +1,6 @@
+%ul
+  - @assays.each do |assay|
+    %li
+      %a{:href => "/aid/#{assay["AID"]}"} #{assay['Assay Name']}
+      AID:
+      = assay["AID"]
diff --git a/views/predicted_targets.haml b/views/predicted_targets.haml
new file mode 100644
index 0000000..1a172ff
--- /dev/null
+++ b/views/predicted_targets.haml
@@ -0,0 +1,6 @@
+%ul
+  - @assays.each do |assay|
+    %li
+      %a{:href => "/aid/#{assay["AID"]}"} #{assay['Target Name']}
+      Target GI:
+      = assay['Target GI']
diff --git a/views/select.haml b/views/select.haml
new file mode 100644
index 0000000..d6e3d20
--- /dev/null
+++ b/views/select.haml
@@ -0,0 +1,8 @@
+%p
+  More than one compound found for
+  = "\"#{params[:name]}\"."
+  Please select a structure:
+- @compounds.each do |compound|
+  %a{:href => "/cid/#{compound.cid}"}
+    %img{:src => compound.image_uri }
+
diff --git a/views/targets.haml b/views/targets.haml
new file mode 100644
index 0000000..1a172ff
--- /dev/null
+++ b/views/targets.haml
@@ -0,0 +1,6 @@
+%ul
+  - @assays.each do |assay|
+    %li
+      %a{:href => "/aid/#{assay["AID"]}"} #{assay['Target Name']}
+      Target GI:
+      = assay['Target GI']