clean before merge

11 files changed, 0 insertions, 532 deletions

diff --git a/views/about.haml b/views/about.haml
deleted file mode 100644
index da0f836..0000000
--- a/views/about.haml
+++ /dev/null
@@ -1,4 +0,0 @@
-%p
-  A demonstration application for the 
-  %a{:href => "http://www.opentox.org"} OpenTox
-  framework.
diff --git a/views/create.haml b/views/create.haml
deleted file mode 100644
index 9477210..0000000
--- a/views/create.haml
+++ /dev/null
@@ -1,17 +0,0 @@
-.upload
-  %form{ :action => url_for('/upload'), :method => "post", :enctype => "multipart/form-data" }
-    %ol
-      %li 
-        %label{:for => 'endpoint'}Enter endpoint name:
-        %input{:type => 'text', :name => 'endpoint', :id => 'endpoint'}
-      %li
-        %label{:for => 'file'}
-          Upload training data in CSV format:
-        %input{:type => 'file', :name => 'file', :id => 'file'}
-        (
-        = link_to "formatting instructions ", 'csv_format'
-        )
-      %li
-        %input{ :type => "submit", :value => "Create model"}
-        = link_to "Cancel", 'create'
-
diff --git a/views/csv_format.haml b/views/csv_format.haml
deleted file mode 100644
index 0943c2f..0000000
--- a/views/csv_format.haml
+++ /dev/null
@@ -1,19 +0,0 @@
-= link_to "Back to model creation", 'create'
-%p
-  The input file should contain two columns, separated by a comma. Enter in the first column the chemical structure in
-  = link_to "SMILES", "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification"
-  format, in the second column the activity classification (1: active, 0: inactive).
-%p Example:
-%p
-  %code
-    %br CC(=O)Nc1ccc(O)cc1, 1  
-    %br O=c1[nH]cnc2[nH]ncc12, 1  
-    %br CCCCNc1cc(cc(c1Oc2ccccc2)S(=O)(=O)N)C(=O)O, 1  
-    %br CC(C)(C)NCC(O)COc1cccc2NC(=O)CCc12, 1  
-    %br CN(C)CCCC1(OCc2cc(C#N)ccc21)c3ccc(F)cc3, 1  
-    %br CCC(CC)CCN1C(=O)CN=C(C2CCCCC2F)c3cc(Cl)ccc13, 0 
-    %br CCN(CC)CC(=O)Nc1c(C)cccc1C, 0 
-    %br CC(C)(C)NCC(O)COc1cccc2CC(O)C(O)Cc12, 0 
-    %br CN1CCCC1c2cccnc2, 0 
-
-%p You can create input files in Excel and export them as CSV files with the "Save As" option from the menu, selecting the CSV (comma delimited) format.
diff --git a/views/delete.haml b/views/delete.haml
deleted file mode 100644
index 88457e0..0000000
--- a/views/delete.haml
+++ /dev/null
@@ -1,25 +0,0 @@
-%hr
-%p
-  You are going to remove the
-  = @model['name']
-  model permanently!
-%p Enter your username/password if you are sure or cancel the operation.
-
-%form{ :action => "/#{params[:id]}", :method => "post" }
-  %input{:type => 'hidden', :name => "_method", :value => "delete"}
-
-  %table
-    %tr
-      %th Username:
-      %td
-        %input{:type => "text", :name => "username"}
-    %tr
-      %th Password:
-      %td
-        %input{:type => "text", :name => "password"}
-
-    %tr
-      %td
-        %input{:type => "submit", :value => "Delete"}
-      %td
-        %a{:href => '/'} Cancel
diff --git a/views/features.haml b/views/features.haml
deleted file mode 100644
index 55f53f3..0000000
--- a/views/features.haml
+++ /dev/null
@@ -1,13 +0,0 @@
-%a{:href => "create"}Select/create dataset
-→ Select endpoint
-%p Dataset #{@dataset_uri} contains more than one endpoint.
-%p Please select an endpoint to predict:
-%form{ :action => 'create', :method => "post" }
-  %input{:type => :hidden, :name => :dataset_uri, :value => @dataset_uri}
-  %p
-    %select{:name => "feature_uri"}
-      - @features.each do |uri,title|
-        %option{:value => uri} #{title}
-  %input{ :type => "submit", :value => "Select"}
-  %a{:href => 'create'} Cancel
-
diff --git a/views/layout.haml b/views/layout.haml
deleted file mode 100644
index 5426c34..0000000
--- a/views/layout.haml
+++ /dev/null
@@ -1,36 +0,0 @@
-!!!
-%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"}
-
-  %head
-    %meta{'http-equiv' => 'Content-Type', :content => 'text/html'}
-    %title ToxModel
-    %link{:rel=>'stylesheet', :href=>'stylesheets/style.css', :type => "text/css"}       
-
-  %body
-    %h1 ToxModel
-
-    .index
-      %ul
-        %li{:class => ("selected" if /create/ =~ request.path )}
-          = link_to "Create", "/create"
-        %li{:class => ("selected" if /predict/ =~ request.path )}
-          = link_to "Predict", "/predict"
-        %li{:class => ("selected" if /tasks/ =~ request.path )}
-          = link_to "Tasks", "/tasks"
-        %li{:class => ("selected" if /about/ =~ request.path )}
-          = link_to "About", "/about"
-
-    .content
-
-      - if flash[:notice]
-        .notice
-          = flash[:notice]
-
-      = yield
-
-    .footer
-      ©
-      %a{:href => 'http://www.in-silico.ch'} in silico toxicology
-      2009, powered by
-      %a{:href => 'http://www.opentox.org'} OpenTox
-
diff --git a/views/predict.haml b/views/predict.haml
deleted file mode 100644
index 7c4b980..0000000
--- a/views/predict.haml
+++ /dev/null
@@ -1,25 +0,0 @@
-.upload
-  - unless @models.nil?
-    %form{ :action => url_for('/predict'), :method => "post", :enctype => "multipart/form-data" }
-      %ol
-        %li
-          %label{:for => 'identifier'}Enter a compound identifier:
-          %input{:type => 'text', :name => 'identifier', :id => 'identifier'}
-          (Name, InChI, Smiles, CAS, ...)
-        %li
-          %label{:for => 'model'}Choose one or more prediction models:
-          %ul
-          - @models.each do |model|
-            - yaml = RestClient.get model, :accept => 'application/x-yaml'
-            - yaml = YAML.load yaml
-            %br
-              -# %input{:type => 'checkbox', :name => 'model_uri', :value => model}
-              -# %input{:type => 'checkbox', :name => "selection[#{model}]", :value => true}
-              %input{:type => 'checkbox', :name => "selection[#{model}]", :value => true, :id => 'model'}
-              = yaml[:endpoint].split(/#/).last
-
-        %li
-          %p
-            %input{ :type => "submit", :value => "Predict"}
-            = link_to 'Cancel', '/' 
-
diff --git a/views/prediction.haml b/views/prediction.haml
deleted file mode 100644
index aa84fee..0000000
--- a/views/prediction.haml
+++ /dev/null
@@ -1,16 +0,0 @@
-%p
-  = link_to "New prediction", "/predict"
-.predictions
-  %table
-    %tr
-      %th
-        %img{:src => @compound.image_uri, :alt => @compound.smiles}
-        %br= @identifier
-      - @predictions.each do |p|
-        %td
-          %b
-            = p[:title] + ":"
-            = p[:prediction]
-          %br
-            Confidence:
-            = p[:confidence]
diff --git a/views/style.sass b/views/style.sass
deleted file mode 100644
index 4d29ddd..0000000
--- a/views/style.sass
+++ /dev/null
@@ -1,92 +0,0 @@
-!bg_color = #FFFFF3
-!fg_color = #36648B
-!body_color = #ECF1EF
-!text_color = black
-
-body
-  background-color = !body_color
-  color = !text_color
-  height: 100%
-  padding: 1em
-  
-  h1
-    text-align: right
-
-  .index
-
-    ul
-      margin: 0
-      padding: 0
-      white-space: nowrap
-      list-style-type: none
-   
-    li
-      margin: 0
-      padding: 0
-      display: inline
-      border-right: 1px solid
-        color = !bg_color
-      border-top: 1px solid
-        color = !bg_color
-      background-color = !fg_color
-      padding-left: 0.5em
-      padding-right: 0.5em
-
-      a
-        text-decoration: none
-        color = !bg_color
-        &:hover
-          color = !bg_color
-    
-    li.selected
-      font-weight: bolder
-      background-color= !bg_color
-      border: 1px solid
-        color = !fg_color
-      border-bottom: 1px solid
-        color = !bg_color
-      a
-        color = !fg_color
-
-
-  .content
-    background-color = !bg_color
-    height: 100%
-    padding: 0.5em
-    border: 1px solid
-      color = !fg_color
-
-    .notice
-      background-color = !body_color
-      margin: 2%
-      padding: 1%
-      border: 1px solid red
-
-    .upload
-      text-align: left
-      form
-        li
-          clear: left
-        label
-          width: 20em
-          float: left
-          margin-right: 0.5em
-          display: block
-
-    .predictions
-      :text-align center
-      table
-        background-color: white
-        :border-spacing 0
-        :border-collapse collapse
-        :margin 0
-        :border 1px solid
-
-        th
-          :border 0
-          :margin 2%
-        td
-          :border 1px solid
-          :padding 2%
-
-  .footer
diff --git a/views/tasks.haml b/views/tasks.haml
deleted file mode 100644
index 3de21b5..0000000
--- a/views/tasks.haml
+++ /dev/null
@@ -1,21 +0,0 @@
-%table
-  %tr
-    %th Task
-    %th Resource
-    %th Status
-    %th Started
-    %th Finished
-  - @tasks.each do |t|
-    -# This is inefficient - make only 1 query to the task service and save variables
-    %tr
-      %td= t.uri
-      %td= t.resource
-      %td= t.status
-      %td= t.created_at
-      %td= t.finished_at
-      -# %td
-        - case t.status
-        - when /created|started/
-          %form{:name => "cancel", :action => url_for("/task/cancel"), :method => 'post'}
-            %input{:type => 'hidden', :name => 'uri', :value => t.uri}
-            %input{:type => "submit", :value => "Cancel"}
diff --git a/views/validation.haml b/views/validation.haml
deleted file mode 100644
index d1af379..0000000
--- a/views/validation.haml
+++ /dev/null
@@ -1,264 +0,0 @@
-= "-> "
-%a{ :href => "/validation/#{params[:id]}" } Validation
-
-%h1
-  = @model['name'].capitalize.gsub(/_/,' ')
-  validation
-
-Created on 
-= @model['created_at']
-by
-= @model['user']
-(
-%a{ :href => @model['validation']['details_uri'] } Prediction details
-)
-
-%h3 Predictions weighted by confidence index
-%p
-  %em Best indication of the overall performance
-
-%table
-  %tr
-    %th
-      True positive predictions
-    %td
-      tp
-    %td
-      = sprintf("%0.2f",@summary[:weighted][:tp].to_f)
-  %tr
-    %th
-      True negative predictions
-    %td
-      tn
-    %td
-      = sprintf("%0.2f",@summary[:weighted][:tn].to_f)
-  %tr
-    %th
-      False positive predictions
-    %td
-      fp
-    %td
-      = sprintf("%0.2f",@summary[:weighted][:fp].to_f)
-  %tr
-    %th
-      False negative predictions
-    %td
-      fn
-    %td
-      = sprintf("%0.2f",@summary[:weighted][:fn].to_f)
-  %tr
-    %th
-      Sensitivity (true positive rate)
-    %td
-      tp/(tp+fn)
-    %td
-      = (100*@summary[:weighted][:tp].to_f/(@summary[:weighted][:tp].to_f+@summary[:weighted][:fn].to_f)).round/100.00
-  %tr
-    %th
-      Specificity (true negative rate)
-    %td
-      tn/(tn+fp)
-    %td
-      = (100*@summary[:weighted][:tn].to_f/(@summary[:weighted][:tn].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
-  %tr
-    %th
-      Positive predictivity
-    %td
-      tp/(tp+fp)
-    %td
-      = (100*@summary[:weighted][:tp].to_f/(@summary[:weighted][:tp].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
-  %tr
-    %th
-      Negative predictivity
-    %td
-      tn/(tn+fn)
-    %td
-      = (100*@summary[:weighted][:tn].to_f/(@summary[:weighted][:tn].to_f+@summary[:weighted][:fn].to_f).to_f).round/100.00
-  %tr
-    %th
-      False positive rate
-    %td
-      fp/(tp+fn)
-    %td
-      = (100*@summary[:weighted][:fp].to_f/(@summary[:weighted][:tp].to_f+@summary[:weighted][:fn].to_f).to_f).round/100.00
-  %tr
-    %th
-      False negative rate
-    %td
-      fn/(tn+fp)
-    %td
-      = (100*@summary[:weighted][:fn].to_f/(@summary[:weighted][:tn].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
-  %tr
-    %th
-      Accuracy (concordance)
-    %td
-      (tp+tn)/(tp+fp+tn+fn)
-    %th
-      = (100*(@summary[:weighted][:tp].to_f+@summary[:weighted][:tn].to_f)/(@summary[:weighted][:tp].to_f+@summary[:weighted][:tn].to_f+@summary[:weighted][:fn].to_f+@summary[:weighted][:fp].to_f).to_f).round/100.00
-
-
-%h3 Predictions within the applicability domain
-%p
-  %em Hard cutoff at confidence > 0.025
-
-%table
-  %tr
-    %th
-      True positive predictions
-    %td
-      tp
-    %td
-      = @summary[:within_ad][:tp].to_i
-  %tr
-    %th
-      True negative predictions
-    %td
-      tn
-    %td
-      = @summary[:within_ad][:tn].to_i
-  %tr
-    %th
-      False positive predictions
-    %td
-      fp
-    %td
-      = @summary[:within_ad][:fp].to_i
-  %tr
-    %th
-      False negative predictions
-    %td
-      fn
-    %td
-      = @summary[:within_ad][:fn].to_i
-  %tr
-    %th
-      Sensitivity (true positive rate)
-    %td
-      tp/(tp+fn)
-    %td
-      = (100*@summary[:within_ad][:tp].to_i/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      Specificity (true negative rate)
-    %td
-      tn/(tn+fp)
-    %td
-      = (100*@summary[:within_ad][:tn].to_i/(@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Positive predictivity
-    %td
-      tp/(tp+fp)
-    %td
-      = (100*@summary[:within_ad][:tp].to_i/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Negative predictivity
-    %td
-      tn/(tn+fn)
-    %td
-      = (100*@summary[:within_ad][:tn].to_i/(@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      False positive rate
-    %td
-      fp/(tp+fn)
-    %td
-      = (100*@summary[:within_ad][:fp].to_i/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      False negative rate
-    %td
-      fn/(tn+fp)
-    %td
-      = (100*@summary[:within_ad][:fn].to_i/(@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Accuracy (concordance)
-    %td
-      (tp+tn)/(tp+fp+tn+fn)
-    %th
-      = (100*(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:tn].to_i)/(@summary[:within_ad][:tp].to_i+@summary[:within_ad][:tn].to_i+@summary[:within_ad][:fn].to_i+@summary[:within_ad][:fp].to_i).to_f).round/100.00
-
-%h3 All predictions
-%p
-  %em Poor indication of the overall performance. Depends predominatly on the fraction of compounds within the applicability domain.
-
-%table
-  %tr
-    %th
-      True positive predictions
-    %td
-      tp
-    %td
-      = @summary[:all][:tp].to_i
-  %tr
-    %th
-      True negative predictions
-    %td
-      tn
-    %td
-      = @summary[:all][:tn].to_i
-  %tr
-    %th
-      False positive predictions
-    %td
-      fp
-    %td
-      = @summary[:all][:fp].to_i
-  %tr
-    %th
-      False negative predictions
-    %td
-      fn
-    %td
-      = @summary[:all][:fn].to_i
-  %tr
-    %th
-      Sensitivity (true positive rate)
-    %td
-      tp/(tp+fn)
-    %td
-      = (100*@summary[:all][:tp].to_i/(@summary[:all][:tp].to_i+@summary[:all][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      Specificity (true negative rate)
-    %td
-      tn/(tn+fp)
-    %td
-      = (100*@summary[:all][:tn].to_i/(@summary[:all][:tn].to_i+@summary[:all][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Positive predictivity
-    %td
-      tp/(tp+fp)
-    %td
-      = (100*@summary[:all][:tp].to_i/(@summary[:all][:tp].to_i+@summary[:all][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Negative predictivity
-    %td
-      tn/(tn+fn)
-    %td
-      = (100*@summary[:all][:tn].to_i/(@summary[:all][:tn].to_i+@summary[:all][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      False positive rate
-    %td
-      fp/(tp+fn)
-    %td
-      = (100*@summary[:all][:fp].to_i/(@summary[:all][:tp].to_i+@summary[:all][:fn].to_i).to_f).round/100.00
-  %tr
-    %th
-      False negative rate
-    %td
-      fn/(tn+fp)
-    %td
-      = (100*@summary[:all][:fn].to_i/(@summary[:all][:tn].to_i+@summary[:all][:fp].to_i).to_f).round/100.00
-  %tr
-    %th
-      Accuracy (concordance)
-    %td
-      (tp+tn)/(tp+fp+tn+fn)
-    %th
-      = (100*(@summary[:all][:tp].to_i+@summary[:all][:tn].to_i)/(@summary[:all][:tp].to_i+@summary[:all][:tn].to_i+@summary[:all][:fn].to_i+@summary[:all][:fp].to_i).to_f).round/100.00