diff options
Diffstat (limited to 'helper.rb')
| -rw-r--r-- | helper.rb | 215 |
1 files changed, 0 insertions, 215 deletions
@@ -1,218 +1,3 @@ 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 => "hide", :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 |