Selection of AMBIT datasets added

8 files changed, 131 insertions, 69 deletions

diff --git a/views/ambit.haml b/views/ambit.haml
new file mode 100644
index 0000000..685c0dc
--- /dev/null
+++ b/views/ambit.haml
@@ -0,0 +1,15 @@
+%b Select:
+= session[:echa].split('#').last
+= "->"
+%b Dataset 
+%em= "-> Prediction Feature"
+
+%form{ :action => url_for('/feature'), :method => "post" }
+  %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
+
+  - @datasets.each do |dataset|
+    %br
+      %input{:type=>'radio', :name => "dataset", :value => dataset} #{OpenTox::Dataset.new(dataset).load_metadata[DC.title]}
+
+  %p
+    %input{:type => 'submit', :value => 'Next'}
diff --git a/views/compound_image.haml b/views/compound_image.haml
index 18944dc..25e0dbf 100644
--- a/views/compound_image.haml
+++ b/views/compound_image.haml
@@ -1,2 +1 @@
 %img{:src => compound.matching_smarts_image_uri(features[:activating].collect{|f| f[:smarts]},features[:deactivating].collect{|f| f[:smarts]}), :alt => compound.to_smiles}
-
diff --git a/views/create.haml b/views/create.haml
index 2149f3d..48669f4 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -17,18 +17,24 @@
     = link_to "instructions for creating training datasets", '/help'
     before submitting.
 
+
   %form{ :action => url_for('/models'), :method => "post", :enctype => "multipart/form-data" }
     %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
     %fieldset
       %label{:for => 'file'}
-        Select training data in
+        Upload training data in
         = link_to "Excel", '/help'
         or
         = link_to "CSV", '/help'
         format:
       %input{:type => 'file', :name => 'file', :id => 'file', :size => '41'}
     %input{ :type => "submit", :value => "Create model"}
-    = link_to "Cancel", '/create'
+    =# link_to "Cancel", '/create'
+
+  %p
+    or
+    %a{:href => "echa"} Select a AMBIT dataset
+    (experimental)
 
   -# explanations
   = haml :lazar_description, :layout => false
diff --git a/views/echa.haml b/views/echa.haml
new file mode 100644
index 0000000..1cabfa0
--- /dev/null
+++ b/views/echa.haml
@@ -0,0 +1,13 @@
+%b Select:
+%b ECHA Endpoint
+%em= "-> Dataset -> Prediction Feature"
+
+%form{ :action => url_for('/ambit'), :method => "post" }
+  %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
+
+  - @endpoints.each do |endpoint|
+    %br
+      %input{:type=>'radio', :name => "endpoint", :value => endpoint} #{endpoint.split('#').last}
+
+  %p
+    %input{:type => 'submit', :value => "Next"}
diff --git a/views/feature.haml b/views/feature.haml
new file mode 100644
index 0000000..c5b8293
--- /dev/null
+++ b/views/feature.haml
@@ -0,0 +1,26 @@
+%b Select:
+= session[:echa].split('#').last
+= "->"
+= OpenTox::Dataset.new(session[:dataset]).load_metadata[DC.title]
+= "->"
+%b Prediction feature
+
+%form{ :action => url_for('/models'), :method => "post" }
+
+  %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
+  %input{:type => 'hidden', :name => 'dataset', :id => 'dataset', :value => session[:dataset]}
+
+  - @features.each do |feature|
+    -# type = "unknown"
+    -# if feature.metadata[RDF.type].include?(OT.NominalFeature)
+      - type = "classification"
+    -# elsif feature.metadata[RDF.type].include?(OT.NumericFeature)
+      - type = "regression"
+
+    %br
+      %input{:type=>'radio', :name => "prediction_feature", :value => feature.uri} #{feature.metadata[DC.title]} (#{feature.feature_type}) 
+    %br
+      =# feature.inspect
+
+  %p
+    %input{:type => 'submit', :value => "Create model"}
diff --git a/views/layout.haml b/views/layout.haml
index c849dec..174db9f 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -17,7 +17,7 @@
       Create and evaluate models to predict toxicity
     .index
       %ul
-        %li{:class => ("selected" if /\/create/ =~ request.path )}
+        %li{:class => ("selected" if /\/create|echa|ambit|feature/ =~ request.path )}
           = link_to "Create", "/create"
         %li{:class => ("selected" if /models/ =~ request.path )}
           = link_to "Inspect", "/models"
@@ -49,5 +49,5 @@
     .footer
       ©
       %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology
-      2009-2010, powered by
+      2009-2011, powered by
       %a{:href => 'http://www.opentox.org', :rel => "external"} <span style="color:#5D308A;font-family:arial,sans-serif,helvetica;letter-spacing:-1px;">Open</span><span style="color:#000;font-family:arial,sans-serif,helvetica;font-weight:bold;letter-spacing:-1px;">Tox</span>
diff --git a/views/lazar.haml b/views/lazar.haml
index deb0c18..6ae6b20 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -1,59 +1,59 @@
-%p= link_to "New prediction", "/predict"

-.lazar-predictions

-

-  -# explanations

-  = haml :lazar_algorithm, :layout => false

-  = haml :confidence, :layout => false

-  = haml :similarity, :layout => false

-  = haml :significant_fragments, :layout => false

-  = haml :training_data, :layout => false

-

-  %a{:name => "prediction"}

-  %table

-    %thead

-      %tr

-        %th= @prediction.title

-        %th= toggle_link("#lazar_algorithm","Prediction")

-        %th= toggle_link("#confidence","Confidence")

-        %th Supporting information

-

-      %tr

-        -# %td

-          %img{:src => @compound.to_image_uri, :alt => @compound.to_smiles}

-        %td.image= compound_image(@compound,@prediction.descriptors(@compound))

-        %td= activity_markup(@prediction.value(@compound))

-        %td= sprintf('%.03g', @prediction.confidence(@compound)) 

-        -#%td= @prediction.confidence(@compound)

-        %td

-          %ul

-            %li

-              %a{:href => "#prediction", :id => "show_names"} Names and synonyms

-              :javascript

-                $("a#show_names").click(function () {

-                  $("#compound_names").load("#{File.join("/compound",@compound.inchi)}");  

-                  $("tr#names").toggle();  

-                });

-            %li= toggle_link("#fragments","Significant fragments")

-            -# This does not work, ask nina/vedrin

-            -# %li

-              %a{:href => "http://ambit.uni-plovdiv.bg:8080/ambit2/query/structure/?search=#{@compound.smiles}", :rel => "external"} Ambit data

-            -# %li

-              %a{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pccompound&term=#{URI.encode('"'+@compound.inchi+'"[InChI]')}", :rel => "external"}  PubChem data

+%p= link_to "New prediction", "/predict"
+.lazar-predictions
+
+  -# explanations
+  = haml :lazar_algorithm, :layout => false
+  = haml :confidence, :layout => false
+  = haml :similarity, :layout => false
+  = haml :significant_fragments, :layout => false
+  = haml :training_data, :layout => false
+
+  %a{:name => "prediction"}
+  %table
+    %thead
+      %tr
+        %th= @prediction.title
+        %th= toggle_link("#lazar_algorithm","Prediction")
+        %th= toggle_link("#confidence","Confidence")
+        %th Supporting information
+
+      %tr
+        -# %td
+          %img{:src => @compound.to_image_uri, :alt => @compound.to_smiles}
+        %td.image= compound_image(@compound,@prediction.descriptors(@compound))
+        %td= activity_markup(@prediction.value(@compound))
+        %td= sprintf('%.03g', @prediction.confidence(@compound)) 
+        -#%td= @prediction.confidence(@compound)
+        %td
+          %ul
+            %li
+              %a{:href => "#prediction", :id => "show_names"} Names and synonyms
+              :javascript
+                $("a#show_names").click(function () {
+                  $("#compound_names").load("#{File.join("/compound",@compound.inchi)}");  
+                  $("tr#names").toggle();  
+                });
+            %li= toggle_link("#fragments","Significant fragments")
+            -# This does not work, ask nina/vedrin
+            -# %li
+              %a{:href => "http://ambit.uni-plovdiv.bg:8080/ambit2/query/structure/?search=#{@compound.smiles}", :rel => "external"} Ambit data
+            -# %li
+              %a{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pccompound&term=#{URI.encode('"'+@compound.inchi+'"[InChI]')}", :rel => "external"}  PubChem data
                 (external)
-            -# %li

-              %a{:href => "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&inchi=#{URI.encode @compound.inchi}", :rel => "external"} ToxNet data

-            -#http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&regno=000143157

-

-      %tr#names{ :style => "display: none;" }

-        %td{:colspan => '4'}

-          %a{:name => 'names'}

-          = hide_link('#names')

-          #compound_names

-      %tr#fragments{ :style => "display: none;" }

-        %td{:colspan => '4'}

-          = hide_link('#fragments')

-          = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(@compound))}, :layout => false

-

-    %tbody#neighbors

-      = haml :neighbors, :locals => {:neighbors => @prediction.neighbors(@compound), :page => @page},  :layout => false

-

+            -# %li
+              %a{:href => "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&inchi=#{URI.encode @compound.inchi}", :rel => "external"} ToxNet data
+            -#http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&regno=000143157
+
+      %tr#names{ :style => "display: none;" }
+        %td{:colspan => '4'}
+          %a{:name => 'names'}
+          = hide_link('#names')
+          #compound_names
+      %tr#fragments{ :style => "display: none;" }
+        %td{:colspan => '4'}
+          = hide_link('#fragments')
+          = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(@compound))}, :layout => false
+
+    %tbody#neighbors
+      = haml :neighbors, :locals => {:neighbors => @prediction.neighbors(@compound), :page => @page},  :layout => false
+
diff --git a/views/model.haml b/views/model.haml
index 4933cdb..b4b3c59 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -58,12 +58,15 @@
       - if model.training_dataset
         %dt Training dataset:
         %dd
-          %a{:href => "#{model.training_dataset}.xls#{subjectstring}"} Excel sheet
-          ,
-          -#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
-          -#%em (experts) ,
-          %a{:href => "#{model.training_dataset}.yaml#{subjectstring}" } YAML
-          %em  (experts)
+          - if model.training_dataset.match(/ambit/i)
+            %a{:href => "#{model.training_dataset}#{subjectstring}", :rel => "external"} Ambit database
+          - else
+            %a{:href => "#{model.training_dataset}.xls#{subjectstring}"} Excel sheet
+            ,
+            -#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
+            -#%em (experts) ,
+            %a{:href => "#{model.training_dataset}.yaml#{subjectstring}" } YAML
+            %em  (experts)
       - if model.feature_dataset
         %dt Feature dataset:
         %dd