update to v3.0.0 and add permission to create models

19 files changed, 222 insertions, 47 deletions

diff --git a/application.rb b/application.rb
index 5137fcc..10507c3 100644
--- a/application.rb
+++ b/application.rb
@@ -90,10 +90,25 @@ get '/login' do
 end
 
 get '/models/?' do
-  @models = ToxCreateModel.all.sort(:order => "DESC")
+  @page = params[:page] ? params[:page].to_i : 0
+  order = params["order"] == "ASC" ? "ASC" : "DESC"
+  params["order"] = order
+  sort_by = params["sort_by"]
+  if sort_by
+    case sort_by
+    when "name", "created_at", "type"
+      @models = ToxCreateModel.all.sort_by(sort_by.to_sym, :order => "#{order} ALPHA")
+    when "id"
+      @models = ToxCreateModel.all.sort(:order => "#{order}")
+    end
+  else
+    params["sort_by"] = "created_at"
+  end
+
+  @models = ToxCreateModel.all.sort(:order => "DESC") unless @models
   @models.each{|m| raise "internal redis error: model is nil" unless m}
-  subjectstring = @subjectid ? "?subjectid=#{CGI.escape(@subjectid)}" : ""
-  haml :models, :locals=>{:models=>@models, :subjectstring => subjectstring}
+  @models.delete_if{|m| !is_authorized(m.web_uri, "GET")}
+  haml :models, :locals=>{:models=>@models}
 end
 
 get '/model/:id/status/?' do
@@ -156,13 +171,12 @@ end
 get '/model/:id/:view/?' do
   response['Content-Type'] = 'text/plain'
   model = ToxCreateModel.get(params[:id])
-  subjectstring = @subjectid ? "?subjectid=#{CGI.escape(@subjectid)}" : ""
   begin
     case params[:view]
       when "model"
-        haml :model, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false
+        haml :model, :locals=>{:model=>model}, :layout => false
       when /validation/
-        haml :validation, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false
+        haml :validation, :locals=>{:model=>model}, :layout => false
       else
         return "unable to render model: id #{params[:id]}, view #{params[:view]}"
     end
@@ -173,6 +187,7 @@ end
 
 get '/predict/?' do 
   @models = ToxCreateModel.all.sort(:order => "DESC")
+  @models.delete_if{|m| !is_authorized(m.web_uri, "GET")}
   @models = @models.collect{|m| m if m.status == 'Completed'}.compact
   haml :predict
 end
@@ -217,7 +232,10 @@ post '/feature' do
 end
 
 post '/models' do # create a new model
-
+  unless is_aluist
+    flash[:notice] = "You do not have the permission to create a new model."
+    redirect url_for('/models')
+  end
   unless (params[:dataset] and params[:prediction_feature]) or (params[:file] and params[:file][:tempfile]) #params[:endpoint] and 
     flash[:notice] = "Please upload a Excel or CSV file or select an AMBIT dataset."
     redirect url_for('/create')
diff --git a/helper.rb b/helper.rb
index 80707c3..20bfa0a 100644
--- a/helper.rb
+++ b/helper.rb
@@ -9,6 +9,10 @@ helpers do
     return false
   end
 
+  def is_aluist
+    OpenTox::Authorization.list_user_groups(session[:username], session[:subjectid]).include?("aluist")
+  end
+
   def hide_link(destination)
     @link_id = 0 unless @link_id
     @link_id += 1
@@ -91,5 +95,29 @@ helpers do
     haml :neighbors_navigation, :layout => false
   end
 
-end
+  def models_navigation
+    @page = 0 unless @page
+    haml :models_navigation, :layout => false
+  end
 
+  def endpoint_option_list(max_time=3600)
+    out = ""
+    tmpfile = File.join(TMP_DIR, "endpoint_option_list")
+    if File.exists? tmpfile
+      if Time.now-File.mtime(tmpfile) <= max_time
+        f = File.open(tmpfile, 'r+')
+        f.each{|line| out << line}
+        return out
+      else
+        File.unlink(tmpfile)
+      end
+    end
+    result = OpenTox::Ontology::Echa.endpoint_option_list()
+    if result.lines.count > 3
+      f = File.new(tmpfile,"w")
+      f.print result
+      f.close
+    end
+    return result
+  end
+end
diff --git a/public/arrow_down.png b/public/arrow_down.png
new file mode 100644
index 0000000..d298656
--- /dev/null
+++ b/public/arrow_down.png
diff --git a/public/arrow_left.png b/public/arrow_left.png
new file mode 100644
index 0000000..8d18c67
--- /dev/null
+++ b/public/arrow_left.png
diff --git a/public/arrow_left_inactive.png b/public/arrow_left_inactive.png
new file mode 100644
index 0000000..52c11bf
--- /dev/null
+++ b/public/arrow_left_inactive.png
diff --git a/public/arrow_right.png b/public/arrow_right.png
new file mode 100644
index 0000000..7fe64a8
--- /dev/null
+++ b/public/arrow_right.png
diff --git a/public/arrow_right_inactive.png b/public/arrow_right_inactive.png
new file mode 100644
index 0000000..496f79e
--- /dev/null
+++ b/public/arrow_right_inactive.png
diff --git a/public/arrow_up.png b/public/arrow_up.png
new file mode 100644
index 0000000..70417dc
--- /dev/null
+++ b/public/arrow_up.png
diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index ee783ce..0e82040 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -18,20 +18,20 @@ $(function() {
     return this.replace(/^\s+|\s+$/g, '');
   }
 
-  checkStati = function(stati, subjectstr) {
+  checkStati = function(stati) {
     stati = stati.split(", ");
     $("body")
     var newstati = new Array;
     $.each(stati, function(){
-      checkProgress(this, subjectstr);
-      if(checkStatus(this, subjectstr) > 0) newstati.push(this);
+      checkProgress(this);
+      if(checkStatus(this) > 0) newstati.push(this);
     });  
-    if (newstati.length > 0) var statusCheck = setTimeout('checkStati("' + newstati.join(", ") + '", "' + subjectstr + '")',10000);
+    if (newstati.length > 0) var statusCheck = setTimeout('checkStati("' + newstati.join(", ") + '")',10000);
   };
   
-  checkStatus = function(id, subjectstr) {
+  checkStatus = function(id) {
     if(id == "") return -1; 
-    var opts = {method: 'get', action: 'model/' + id + '/status' + subjectstr, id: id};
+    var opts = {method: 'get', action: 'model/' + id + '/status', id: id};
     var status_changed = $.ajax({
       type: opts.method,
       url: opts.action,
@@ -62,7 +62,7 @@ $(function() {
   };
   
   
-  checkProgress = function(id, subjectstr) {
+  checkProgress = function(id) {
     var task = $("input#model_" + id + "_task").attr('value');
     var opts = {action: task + "/percentageCompleted" , id: id};
     var progress_changed = $.ajax({
diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index 47e1f75..e06cb65 100644
--- a/views/classification_validation.haml
+++ b/views/classification_validation.haml
@@ -5,13 +5,24 @@
 %dt
   %a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :rel => "external"} Average area under ROC:
 %dd 
-  = sprintf("%.3f", model.average_area_under_roc.to_f) if model.average_area_under_roc
+  - if model.average_area_under_roc
+    = sprintf("%.3f", model.average_area_under_roc.to_f)
+  - else
+    = 'NA'
 %dt
   %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Specificity:
-%dd= sprintf("%.3f", model.specificity.to_f) if model.specificity
+%dd
+  - if model.specificity
+    = sprintf("%.3f", model.specificity.to_f)
+  - else
+    = 'NA'
 %dt
   %a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :rel => "external"} Sensitivity:
-%dd= sprintf("%.3f", model.sensitivity.to_f) if model.sensitivity
+%dd
+  - if model.sensitivity
+    = sprintf("%.3f", model.sensitivity.to_f)
+  - else
+    = 'NA'
 %dt
   %a{:href => "http://en.wikipedia.org/wiki/Confusion_matrix", :rel => "external"} Confusion Matrix:
 - if model.confusion_matrix
diff --git a/views/create.haml b/views/create.haml
index b706484..da85382 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -24,6 +24,8 @@
         = link_to "SDF", '/help'
         format:
       %input{:type => 'file', :name => 'file', :id => 'file', :size => '41'}
+      %br
+      -# = haml :model_echa, :layout => false
     %input{ :type => "submit", :value => "Create model"}
     =# link_to "Cancel", '/create'
 
@@ -47,15 +49,16 @@
     structure-activity models from your experimental data. The models can be used to predict toxicity of new chemicals (e.g. for 
     %a{:href => "http://ec.europa.eu/environment/chemicals/reach/reach_intro.htm", :rel => "external"} REACH
     purposes) and to reduce the need for animal testing.  The following methods are currently available:
-    %ul
-      %li
-        = toggle_link("#lazar_description","lazar")
-        %em= toggle_link("#classification","classification")
-        models and
-      %li
-        = toggle_link("#lazar_description","lazar")
-        %em= toggle_link("#regression","regression")
-        models (experimental) 
+  %ul
+    %li
+      = toggle_link("#lazar_description","lazar")
+      %em= toggle_link("#classification","classification")
+      models and
+    %li
+      = toggle_link("#lazar_description","lazar")
+      %em= toggle_link("#regression","regression")
+      models (experimental)
+  %p
     Further modelling algorithms may be added in future versions.
 
   .login_notice
diff --git a/views/endpoint.haml b/views/endpoint.haml
index af06b80..9c250ca 100644
--- a/views/endpoint.haml
+++ b/views/endpoint.haml
@@ -9,4 +9,4 @@
     %em in-vitro,
     or
     %em in-vivo
-    expriment, clinical trial or epidemiological study
+    experiment, clinical trial or epidemiological study
diff --git a/views/model.haml b/views/model.haml
index 266fe19..51a7498 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -25,8 +25,14 @@
               });
               
             %div{:id => "model_#{model.id}_progress", :class => "model_progress", :title => "#{percentage_completed}%"}
-              //= haml :model_progress, :locals=>{:percentage_completed=>percentage_completed}, :layout => false        
-       
+              //= haml :model_progress, :locals=>{:percentage_completed=>percentage_completed}, :layout => false
+
+        - if is_authorized(model.web_uri, "DELETE")
+          %a{:href => url_for("/model/#{model.id}"), :id => "delete_#{model.id}", :class => 'delete_link'}
+            - if model.status =~ /Completed|Error|Cancelled/ 
+              &nbsp;(delete)
+            - else
+              &nbsp;(stop)
         %span
           %br
         
@@ -38,7 +44,7 @@
       - if model.error_messages
         %dt Errors:
         %dd= model.error_messages
-      - if CONFIG[:logger]=="debug"
+      - if CONFIG[:logger]=="debug" && is_aluist
         %dt Task:
         %dd
           %a{:href => "#{model.task_uri}", :id => "model_#{model.id}_task_link", :rel => "external"}
@@ -60,26 +66,26 @@
         %dt Training dataset:
         %dd
           - if model.training_dataset.match(/ambit/i)
-            %a{:href => "#{model.training_dataset}#{subjectstring}", :rel => "external"} Ambit database
+            %a{:href => "#{model.training_dataset}", :rel => "external"} Ambit database
           - else
-            %a{:href => "#{model.training_dataset}.xls#{subjectstring}"} Excel sheet
+            %a{:href => "#{model.training_dataset}.xls"} Excel sheet
             ,
             -#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
             -#%em (experts) ,
-            %a{:href => "#{model.training_dataset}.sdf#{subjectstring}" } SDF
+            %a{:href => "#{model.training_dataset}.sdf" } SDF
             ,
-            %a{:href => "#{model.training_dataset}.yaml#{subjectstring}" } YAML
+            %a{:href => "#{model.training_dataset}.yaml" } YAML
             %em  (experts)
       - if model.feature_dataset
         %dt Feature dataset:
         %dd
           -#%a{:href => "#{model.feature_dataset}.rdf"} RDF/XML
           -#,
-          %a{:href => "#{model.feature_dataset}.xls#{subjectstring}"} Excel sheet
+          %a{:href => "#{model.feature_dataset}.xls"} Excel sheet
           ,
-          %a{:href => "#{model.feature_dataset}.sdf#{subjectstring}"} SDF
+          %a{:href => "#{model.feature_dataset}.sdf"} SDF
           ,
-          %a{:href => "#{model.feature_dataset}.yaml#{subjectstring}"} YAML
+          %a{:href => "#{model.feature_dataset}.yaml"} YAML
           %em  (experts)
       - if model.uri
         %dt Model:
@@ -89,7 +95,7 @@
           -#,
           - if model.validation_qmrf_uri
             %a{:href => File.join(model.validation_qmrf_uri,"editor")} QMRF Editor, 
-          %a{:href => "#{model.uri}.yaml#{subjectstring}"} YAML
+          %a{:href => "#{model.uri}.yaml"} YAML
           %em  (experts, models cannot be represented in Excel)
 
-    = haml :validation, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false     
+    = haml :validation, :locals=>{:model=>model}, :layout => false
diff --git a/views/model_echa.haml b/views/model_echa.haml
new file mode 100644
index 0000000..257a28a
--- /dev/null
+++ b/views/model_echa.haml
@@ -0,0 +1,2 @@
+Select an endpoint:
+= endpoint_option_list
\ No newline at end of file
diff --git a/views/model_name.haml b/views/model_name.haml
index 874ddaa..19819f4 100644
--- a/views/model_name.haml
+++ b/views/model_name.haml
@@ -5,4 +5,8 @@
   });
 %h2
   = model.name
-  
+  - if is_authorized(model.web_uri, "PUT")
+    %span{:class => "edit_button"}
+      (
+      %a{:href => url_for("/model/#{model.id}/name?mode=edit"), :id => "edit_#{model.id}"} edit
+      )
diff --git a/views/models.haml b/views/models.haml
index 9b70ae7..947e403 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -3,7 +3,7 @@
 :javascript
   $(function() {
     if(#{stati != 0}) { 
-      setTimeout('checkStati("#{stati_to_check}", "#{subjectstring}")',5000);
+      setTimeout('checkStati("#{stati_to_check}", "")',5000);
     }
     var reload_validation = true;
   });
@@ -18,8 +18,11 @@
 = haml :similarity, :layout => false
 = haml :significant_fragments, :layout => false
 
-- if @models
-  - @models.each do |model|
-    = haml :model, :locals=>{:model=>model,:subjectstring=>subjectstring}, :layout => false 
--if @models.size == 0 
+- first = 5*@page
+- last = first+4
+= models_navigation if @models.size > 1
+- if @models[first..last]
+  - @models[first..last].each do |model|
+    = haml :model, :locals=>{:model=>model}, :layout => false
+-if @models.size == 0
   .notice There are currently no models. You have to create a model first.
diff --git a/views/models_navigation.haml b/views/models_navigation.haml
new file mode 100644
index 0000000..0dc1f63
--- /dev/null
+++ b/views/models_navigation.haml
@@ -0,0 +1,70 @@
+.models_navigation
+
+  %form{:name => "nav", :action => url_for('/models'), :method => "get", :id => "nav"}
+    %input{:type => :hidden, :name => :sort_by, :id => "sort_by", :value => params[:sort_by]}
+    %input{:type => :hidden, :name => :order, :id => "order", :value => params[:order]}
+    %input{:type => :hidden, :name => :page, :id => "page", :value => params[:page]}
+
+    Sort by:
+    - ["created_at","name","type"].each do |s|
+      - idname = s == "created_at" ? "date" : s
+      - if params[:sort_by] == s
+        %div{:id => idname, :class => "active"}
+          %span="#{idname.capitalize}"
+          - if params[:order] == "ASC"
+            #up{:class => "link"}
+              %img{:src => "arrow_down.png", :alt => 'in ascending order', :title => 'in ascending order'}/
+          - else
+            #down{:class => "link"}
+              %img{:src => "arrow_up.png", :alt => 'in descending order', :title => 'in descending order'}/
+      - else
+        %div{:id => idname, :class => "link"}="#{idname.capitalize}&nbsp;"
+    - if @models.size > 5
+      |
+      Models:
+      = "#{@models.size}"
+      - unless @page.to_i == 0
+        #prev
+          %img{:src => "arrow_left.png", :alt => 'previous', :title => 'previous'}/
+      -else
+        %img{:src => "arrow_left_inactive.png", :alt => '', :title => ''}/
+  
+      - if @models.size < 5*@page+5
+        - last = @models.size
+      - else
+        - last = 5*@page+5
+  
+      = "(#{5*@page+1}-#{last}/#{@models.size})"
+      - unless 5*@page.to_i+5 >= @models.size
+        #next
+          %img{:src => "arrow_right.png", :alt => 'next', :title => 'next'}/
+      -else
+        %img{:src => "arrow_right_inactive.png", :alt => '', :title => ''}/
+
+    - js = ""
+    - ["created_at","name","type"].each do |s|
+      - idname = s == "created_at" ? "date" : s
+      - js += "$('##{idname}').click(function() \{ \n "
+      - js += "  $('#sort_by').val('#{s}');\n "
+      - js += "  $('#nav').submit();\n "
+      - js += "});\n "
+
+    :javascript
+      $("#prev").click(function() {
+        $("#page").val(#{@page-1});
+        $("#nav").submit();
+      });
+      $("#next").click(function() {
+        $("#page").val(#{@page+1});
+        $("#nav").submit();
+      });
+      #{js}
+      $("#down").click(function() {
+        $("#order").val("ASC");
+        $("#nav").submit();
+      });
+      $("#up").click(function() {
+        $("#order").val("DESC");
+        $("#nav").submit();
+      });
+      
\ No newline at end of file
diff --git a/views/style.sass b/views/style.sass
index 9f1bf5b..ab05d93 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -281,3 +281,33 @@ dl
   margin-left: 16px
   margin-right: 16px
   float: left
+
+.models_navigation
+  #prev
+    @extend a
+    display: inline
+    cursor: pointer
+  #next
+    @extend a
+    display: inline
+    cursor: pointer
+  .link
+    @extend a
+    display: inline
+    cursor: pointer
+  .active
+    display: inline
+    color: #000
+    font-weight: bold
+  .thin
+    font-weight: 100
+
+.level_1
+  padding-left: 10px
+  font-weight: bold
+.level_2
+  padding-left: 20px
+.level_3
+  padding-left: 30px
+.level_4
+  padding-left: 40px
diff --git a/views/validation.haml b/views/validation.haml
index b8a6eaa..0a094d6 100644
--- a/views/validation.haml
+++ b/views/validation.haml
@@ -7,7 +7,7 @@
         - if model.validation_report_uri
           %dt Detailed report:
           %dd
-            %a{:href => model.validation_report_uri + subjectstring, :target => "_blank"} show
+            %a{:href => model.validation_report_uri, :target => "_blank"} show
         %dt Number of predictions:
         %dd= model.nr_predictions.to_s
         - case model.type