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|
include OpenTox
configure :production do
$logger = Logger.new(STDOUT)
enable :reloader
end
configure :development do
$logger = Logger.new(STDOUT)
enable :reloader
end
before do
@version = File.read("VERSION").chomp
end
not_found do
redirect to('/predict')
end
error do
@error = request.env['sinatra.error']
haml :error
end
helpers do
def embedded_svg image, options={}
doc = Nokogiri::HTML::DocumentFragment.parse image
svg = doc.at_css 'svg'
title = doc.at_css 'title'
if options[:class].present?
svg['class'] = options[:class]
end
if options[:title].present?
title.children.remove
text_node = Nokogiri::XML::Text.new(options[:title], doc)
title.add_child(text_node)
end
doc.to_html.html_safe
end
end
get '/?' do
redirect to('/predict')
end
get '/predict/?' do
@models = Model::Validation.all
@models = @models.delete_if{|m| m.model.name =~ /\b(Net cell association)\b/}
@endpoints = @models.collect{|m| m.endpoint}.sort.uniq
@endpoints << "Oral toxicity (Cramer rules)"
@models.count <= 0 ? (haml :info) : (haml :predict)
end
get '/predict/modeldetails/:model' do
model = Model::Validation.find params[:model]
crossvalidations = Validation::RepeatedCrossValidation.find(model.repeated_crossvalidation_id).crossvalidations
return haml :model_details, :layout=> false, :locals => {:model => model, :crossvalidations => crossvalidations}
end
get '/jme_help/?' do
File.read(File.join('views','jme_help.html'))
end
get '/predict/dataset/:name' do
response['Content-Type'] = "text/csv"
dataset = Dataset.find_by(:name=>params[:name])
csv = dataset.to_csv
csv
end
get '/predict/:tmppath/:model/:filename?' do
response['Content-Type'] = "text/csv"
path = File.join("tmp", params[:tmppath])
`sort -gk1 #{path} -o #{path}`
send_file path, :filename => "#{Time.now.strftime("%Y-%m-%d")}_lazar_batch_prediction_#{params[:model]}_#{params[:filename]}", :type => "text/csv", :disposition => "attachment"
end
get '/batch/:model/' do
if params[:model] == "Cramer"
dataset = Dataset.find params[:dataset]
compounds = dataset.compounds.collect{|c| c.smiles}
prediction = [Toxtree.predict(compounds, "Cramer rules"), Toxtree.predict(compounds, "Cramer rules with extensions")]
output = {}
output["model_name"] = "Oral toxicity (Cramer rules)"
output["model_type"] = false
output["model_unit"] = false
["measurements", "converted_measurements", "prediction_value", "converted_value", "interval", "converted_interval", "probability", "db_hit", "warnings", "info", "toxtree", "sa_prediction", "sa_matches", "confidence"].each do |key|
output["#{key}"] = false
end
output["toxtree"] = true
output["cramer_rules"] = prediction.collect{|array| array.collect{|hash| hash["Cramer rules"]}}.flatten.compact
output["cramer_rules_extensions"] = prediction.collect{|array| array.collect{|hash| hash["Cramer rules, with extensions"]}}.flatten.compact
# td paths to insert results in GUI
compound_ids = dataset.compounds.collect{|c| c.id}
output["tds"] = compound_ids.each_with_index.map{|cid,idx| "prediction_#{cid}_Cramer_#{idx}"}
# write to file
# header
csv = "ID,Endpoint,Unique SMILES,Cramer rules,Cramer rules with extensions\n"
compounds.each_with_index do |smiles, idx|
csv << "#{idx+1},#{output["model_name"]},#{smiles},"\
"#{output["cramer_rules"][idx] != "nil" ? output["cramer_rules"][idx] : "none" },"\
"#{output["cramer_rules_extensions"][idx] != "nil" ? output["cramer_rules_extensions"][idx] : "none"}\n"
end
File.open(File.join("tmp", params[:tmppath]),"a+"){|file| file.write(csv)}
# cleanup
dataset.delete
# return output
response['Content-Type'] = "application/json"
return JSON.pretty_generate output
else
idx = params[:idx].to_i
compound = Compound.find params[:compound]
model = Model::Validation.find params[:model]
prediction = model.predict(compound)
output = {}
output["model_name"] = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
output["model_type"] = model.model.class.to_s.match("Classification") ? type = "Classification" : type = "Regression"
output["model_unit"] = (type == "Regression") ? "(#{model.unit})" : ""
output["converted_model_unit"] = (type == "Regression") ? "#{model.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : ""
["measurements", "converted_measurements", "prediction_value", "converted_value", "interval", "converted_interval", "probability", "db_hit", "warnings", "info", "toxtree", "sa_prediction", "sa_matches", "confidence"].each do |key|
output["#{key}"] = false
end
if prediction[:value]
inApp = (prediction[:warnings].join(" ") =~ /Cannot/ ? "no" : (prediction[:warnings].join(" ") =~ /may|Insufficient/ ? "maybe" : "yes"))
if prediction[:info] =~ /\b(identical)\b/i
prediction[:info] = "This compound was part of the training dataset. All information "\
"from this compound was removed from the training data before the "\
"prediction, to obtain unbiased results."
end
note = "\"#{prediction[:warnings].uniq.join(" ")}\""
output["prediction_value"] = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)}" : "#{prediction[:value]}"
output["converted_value"] = "#{compound.mmol_to_mg(prediction[:value].delog10).signif(3)}" if type == "Regression"
output["db_hit"] = prediction[:info] if prediction[:info]
if prediction[:measurements].is_a?(Array)
output["measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{model.unit})"} : prediction[:measurements].collect{|value| "#{value}"}
output["converted_measurements"] = (type == "Regression") ? prediction[:measurements].collect{|value| "#{compound.mmol_to_mg(value.delog10).signif(3)} #{model.unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"} : false
else
output["measurements"] = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{model.unit})}" : "#{prediction[:measurements]}"
output["converted_measurements"] = (type == "Regression") ? "#{compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(model.unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : false
end #db_hit
if type == "Regression"
if !prediction[:prediction_interval].nil?
interval = prediction[:prediction_interval]
output['interval'] = "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)}"
output['converted_interval'] = "#{compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{compound.mmol_to_mg(interval[0].delog10).signif(3)}"
end #prediction interval
csv = "#{idx+1},#{output['model_name']},#{compound.smiles},"\
"\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{prediction[:measurements].join("; ") if prediction[:info]}\","\
"#{output['prediction_value'] != false ? output['prediction_value'] : ""},"\
"#{output['converted_value'] != false ? output['converted_value'] : ""},"\
"#{output['interval'].split(" - ").first.strip unless output['interval'] == false},"\
"#{output['interval'].split(" - ").last.strip unless output['interval'] == false},"\
"#{output['converted_interval'].split(" - ").first.strip unless output['converted_interval'] == false},"\
"#{output['converted_interval'].split(" - ").last.strip unless output['converted_interval'] == false},"\
"#{inApp},#{note.nil? ? "" : note.chomp}\n"
else # Classification
# consensus mutagenicity
sa_prediction = KaziusAlerts.predict(compound.smiles)
lazar_mutagenicity = prediction
confidence = 0
lazar_mutagenicity_val = (lazar_mutagenicity[:value] == "non-mutagenic" ? false : true)
if sa_prediction[:prediction] == false && lazar_mutagenicity_val == false
confidence = 0.85
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == true
confidence = 0.85 * ( 1 - sa_prediction[:error_product] )
elsif sa_prediction[:prediction] == false && lazar_mutagenicity_val == true
confidence = 0.11
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == false
confidence = ( 1 - sa_prediction[:error_product] ) - 0.57
end
output['sa_prediction'] = sa_prediction
output['sa_matches'] = sa_prediction[:matches].collect{|a| a.first}.join("; ") unless sa_prediction[:matches].blank?
output['confidence'] = confidence.signif(3)
output['model_name'] = "Lazar #{model.endpoint.gsub('_', ' ').downcase} (#{model.species}):"
output['probability'] = prediction[:probabilities] ? prediction[:probabilities].collect{|k,v| "#{k}: #{v.signif(3)}"} : false
csv = "#{idx+1},Consensus mutagenicity,#{compound.smiles},"\
"\"#{prediction[:info] ? prediction[:info] : "no"}\",\"#{prediction[:measurements].join("; ") if prediction[:info]}\","\
"#{sa_prediction[:prediction] == false ? "non-mutagenic" : "mutagenic"},"\
"#{output['confidence']},#{output['sa_matches'] != false ? "\"#{output['sa_matches']}\"" : "none"},"\
"#{output['prediction_value']},"\
"#{output['probability'][0] != false ? output['probability'][0].split(":").last : ""},"\
"#{output['probability'][1] != false ? output['probability'][1].split(":").last : ""},"\
"#{inApp},#{note.nil? ? "" : note}\n"
end
output["warnings"] = prediction[:warnings] if prediction[:warnings]
else #no prediction value
inApp = "no"
if prediction[:info] =~ /\b(identical)\b/i
prediction[:info] = "This compound was part of the training dataset. All information "\
"from this compound was removed from the training data before the "\
"prediction, to obtain unbiased results."
end
note = "\"#{prediction[:warnings].join(" ")}\""
output["warnings"] = prediction[:warnings]
output["info"] = prediction[:info] if prediction[:info]
if type == "Regression"
csv = "#{idx+1},#{output['model_name']},#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
"#{prediction[:measurements] if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
else
csv = "#{idx+1},Consensus mutagenicity,#{compound.smiles},#{prediction[:info] ? prediction[:info] : "no"},"\
"#{prediction[:measurements] if prediction[:info]},,,,,,,"+ [inApp,note].join(",")+"\n"
end
end #prediction value
# write to file
File.open(File.join("tmp", params[:tmppath]),"a"){|file| file.write(csv)}
# return output
response['Content-Type'] = "application/json"
return JSON.pretty_generate output
end# if Cramer
end
post '/predict/?' do
# process batch prediction
if !params[:fileselect].blank?
if params[:fileselect][:filename] !~ /\.csv$/
bad_request_error "Please submit a csv file."
end
File.open('tmp/' + params[:fileselect][:filename], "w") do |f|
f.write(params[:fileselect][:tempfile].read)
end
@filename = params[:fileselect][:filename]
begin
input = Dataset.from_csv_file File.join("tmp", params[:fileselect][:filename]), true
$logger.debug "save dataset #{params[:fileselect][:filename]}"
if input.class == OpenTox::Dataset
@dataset = Dataset.find input
@compounds = @dataset.compounds
else
bad_request_error "Could not serialize file '#{@filename}'."
end
rescue
bad_request_error "Could not serialize file '#{@filename}'."
end
if @compounds.size == 0
message = dataset[:warnings]
@dataset.delete
bad_request_error message
end
@models = params[:selection].keys
@tmppaths = {}
@models.each do |model|
m = Model::Validation.find model
type = (m.regression? ? "Regression" : "Classification") unless model == "Cramer"
# add header for regression
if type == "Regression"
unit = (type == "Regression") ? "(#{m.unit})" : ""
converted_unit = (type == "Regression") ? "#{m.unit =~ /\b(mmol\/L)\b/ ? "(mg/L)" : "(mg/kg_bw/day)"}" : ""
header = "ID,Endpoint,Unique SMILES,inTrainingSet,Measurements,Prediction #{unit},Prediction #{converted_unit},"\
"Prediction Interval Low #{unit},Prediction Interval High #{unit},"\
"Prediction Interval Low #{converted_unit},Prediction Interval High #{converted_unit},"\
"inApplicabilityDomain,Note\n"
end
# add header for classification
if type == "Classification"
av = m.prediction_feature.accept_values
header = "ID,Endpoint,Unique SMILES,inTrainingSet,Measurements,Consensus Prediction,Consensus Confidence,"\
"Structural alerts for mutagenicity,Lazar Prediction,"\
"Lazar predProbability #{av[0]},Lazar predProbability #{av[1]},inApplicabilityDomain,Note\n"
end
path = File.join("tmp", "#{Time.now.strftime("%Y-%m-%d")}_#{SecureRandom.urlsafe_base64(5)}")
File.open(path, "w"){|f| f.write(header) if header}
@tmppaths[model] = path.split("/").last
end
File.delete File.join("tmp", params[:fileselect][:filename])
return haml :batch
end
# single compound prediction
# validate identifier input
if !params[:identifier].blank?
@identifier = params[:identifier].strip
$logger.debug "input:#{@identifier}"
# get compound from SMILES
@compound = Compound.from_smiles @identifier
bad_request_error "'#{@identifier}' is not a valid SMILES string." if @compound.blank?
@models = []
@predictions = []
@toxtree = false
params[:selection].keys.each do |model_id|
if model_id == "Cramer"
@toxtree = true
@predictions << [Toxtree.predict(@compound.smiles, "Cramer rules"), Toxtree.predict(@compound.smiles, "Cramer rules with extensions")]
else
model = Model::Validation.find model_id
@models << model
if model.model.name =~ /kazius/
sa_prediction = KaziusAlerts.predict(@compound.smiles)
lazar_mutagenicity = model.predict(@compound)
confidence = 0
lazar_mutagenicity_val = (lazar_mutagenicity[:value] == "non-mutagenic" ? false : true)
if sa_prediction[:prediction] == false && lazar_mutagenicity_val == false
confidence = 0.85
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == true
confidence = 0.85 * ( 1 - sa_prediction[:error_product] )
elsif sa_prediction[:prediction] == false && lazar_mutagenicity_val == true
confidence = 0.11
elsif sa_prediction[:prediction] == true && lazar_mutagenicity_val == false
confidence = ( 1 - sa_prediction[:error_product] ) - 0.57
end
@predictions << [lazar_mutagenicity, {:prediction => sa_prediction, :confidence => confidence}]
else
@predictions << model.predict(@compound)
end
end
end
haml :prediction
end
end
get '/style.css' do
headers 'Content-Type' => 'text/css; charset=utf-8'
scss :style
end
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