first commit

1 files changed, 218 insertions, 0 deletions

diff --git a/helper.rb b/helper.rb
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+++ b/helper.rb
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+helpers do
+
+  def is_authorized(uri, action)
+    if OpenTox::Authorization.server && session[:subjectid] != nil
+      return OpenTox::Authorization.authorized?(uri, action, session[:subjectid])
+    else
+      return true
+    end
+    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
+    haml :js_link, :locals => {:name => "close", :destination => destination, :method => "hide"}, :layout => false
+  end
+
+  def toggle_link(destination,name)
+    @link_id = 0 unless @link_id
+    @link_id += 1
+    haml :js_link, :locals => {:name => name, :destination => destination, :method => "toggle"}, :layout => false
+  end
+
+  def sort(descriptors,value_map)
+    features = {:activating => [], :deactivating => [], :pc_features => []}
+    if descriptors.kind_of?(Array)
+      descriptors.each do |d|
+        if !value_map.empty?
+          features[:activating] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} if d[OT.effect] == 2
+          features[:deactivating] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} if d[OT.effect] == 1
+        else
+          if d[OT.effect] =~ TRUE_REGEXP 
+            features[:activating] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} 
+          elsif d[OT.effect] =~ FALSE_REGEXP 
+            features[:deactivating] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} 
+          end
+        end
+      end
+    else
+      descriptors.each do |d,v|
+        features[:pc_features] << {:feature => d, :value => v}
+      end
+    end
+    features
+  end
+
+  def compound_image(compound,descriptors,value_map)
+    haml :compound_image, :locals => {:compound => compound, :features => sort(descriptors,value_map)}, :layout => false
+  end
+  
+  def activity_markup(activity,value_map)
+    if value_map and !value_map.empty?
+      if value_map.size == 2
+        activity = value_map.index(activity) if value_map.has_value? activity
+        if activity.to_i == 2
+          haml ".active #{value_map[activity]}", :layout => false
+        elsif activity.to_i == 1
+          haml ".inactive #{value_map[activity]}", :layout => false
+        else
+          haml ".other #{activity.to_s}", :layout => false
+        end
+      else
+        haml ".other #{activity.to_s}", :layout => false
+      end
+    elsif OpenTox::Algorithm::numeric? activity
+      haml ".other #{sprintf('%.03g', activity.to_f)}", :layout => false
+    else
+      haml ".other #{activity.to_s}", :layout => false
+    end
+=begin
+    case activity.class.to_s
+    when /Float/
+      haml ".other #{sprintf('%.03g', activity)}", :layout => false
+    when /String/
+      case activity
+      when "true"
+        haml ".active active", :layout => false
+      when "false"
+        haml ".inactive inactive", :layout => false
+      else
+        haml ".other #{activity.to_s}", :layout => false
+      end
+    else 
+      if activity #true
+        haml ".active active", :layout => false
+      elsif !activity # false
+        haml ".inactive inactive", :layout => false
+      else
+        haml ".other #{activity.to_s}", :layout => false
+      end
+    end
+=end
+  end
+
+  def neighbors_navigation
+    @page = 0 unless @page
+    haml :neighbors_navigation, :layout => false
+  end
+
+  def models_navigation
+    @page = 0 unless @page
+    haml :models_navigation, :layout => false
+  end
+
+  def models_navigation_bottom
+    @page = 0 unless @page
+    haml :models_navigation_bottom, :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 = endpoint_selection()
+    if result.lines.count > 3
+      f = File.new(tmpfile,'w')
+      f.print result
+      f.close
+    end
+    result
+  end
+
+  def endpoint_level(endpoint="Endpoints", level=1)
+    results = OpenTox::Ontology::Echa.echa_endpoints(endpoint) rescue results = []
+    out = ""
+    out += "<ul id='list_#{endpoint}' class='endpoint level_#{level}'>\n" if results.size > 0
+    results.each do |result|
+      r = result.split(',')
+      endpointname = CGI.escape(r.first.split("#").last).gsub(".","")
+      title = r[1..r.size-1].to_s
+      out += "  <li class='level_#{level}'><input type='radio' name='endpoint' value='#{result}' id='#{endpointname}' class='endpoint_list' /><label for='#{endpointname}' id='label_#{endpointname}'>#{title.gsub("\"","")}</label>\n"
+      out += endpoint_level(endpointname, level + 1)
+      out += "</li>\n"
+    end
+    out += "</ul>\n" if results.size > 0
+    return out
+  end
+
+  def endpoint_selection()
+    out = "<span id='endpoint_label'></span><input type='button' id='endpoint_list_button' value='Select endpoint' /> \n
+    <div id='div_endpoint'>\n"
+    out += "<b>Please select:</b>\n"
+    out += endpoint_level
+    js = ""
+    out += "</div>\n"
+    return out
+  end
+
+  def logmmol_to_mg(value ,mw)
+    mg = round_to((10**(-1.0*round_to(value.to_f, 2))*(mw.to_f*1000)),4)
+    return mg
+  end
+
+  def logmg_to_mg(value)
+    mg = round_to(10**round_to(value.to_f, 2),4)
+    return mg
+  end
+
+  def ptd50_to_td50(value ,mw)
+    td50 = round_to((10**(-1.0*round_to(value.to_f, 2))*(mw.to_f*1000)),4)
+    return td50   
+  end
+
+  def round_to(value, deci)
+    rounded = (value.to_f*(10**deci)).round / (10**deci).to_f
+    return rounded
+  end
+
+  def calc_mw(compound_uri)
+    ds = OpenTox::Dataset.new()
+    ds.save(@subjectid)
+    ds.add_compound(compound_uri)
+    ds.save(@subjectid)
+    mw_algorithm_uri = File.join(CONFIG[:services]["opentox-algorithm"],"pc/MW")
+    mw_uri = OpenTox::RestClientWrapper.post(mw_algorithm_uri, {:dataset_uri=>ds.uri})
+    ds.delete(@subjectid)
+    mw_ds = OpenTox::Dataset.find(mw_uri, @subjectid)
+    mw = mw_ds.data_entries[compound_uri][mw_uri.to_s + "/feature/MW"].first.to_f
+    mw_ds.delete(@subjectid)
+    return mw 
+  end
+
+  def transform(value, compound_uri, name, haml)
+    prediction_trans = nil
+    model_name = name.to_s.downcase
+    if model_name.include? "ptd50"
+      mw = calc_mw(compound_uri)
+      td50 = ptd50_to_td50(value, mw)
+      prediction_trans = "TD50: #{td50}"
+    elsif model_name.include? "loael"
+      if model_name.include? "mol"
+        mw = calc_mw(compound_uri)
+        mg = logmmol_to_mg(value, mw)
+        prediction_trans = "mg/kg bw/day: #{mg}"
+      elsif model_name.include? "mg"
+        mg = logmg_to_mg(value)
+        prediction_trans = "mg/kg bw/day: #{mg}"
+      end
+    end
+    if haml == true
+      haml ".other #{prediction_trans.to_s}", :layout => false
+    else
+      return prediction_trans
+    end
+  end
+end