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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 => "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
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