diff options
Diffstat (limited to 'application.rb')
| -rw-r--r-- | application.rb | 135 |
1 files changed, 85 insertions, 50 deletions
diff --git a/application.rb b/application.rb index baba620..3e7dfc2 100644 --- a/application.rb +++ b/application.rb @@ -5,6 +5,11 @@ $ambit_search = "http://data.enanomapper.net/substance?type=name&search=" include OpenTox +# collect nanoparticles from training dataset (Au + Ag) +dataset = Dataset.find_by(:name=> "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles") +$nanoparticles = dataset.nanoparticles +$coating_list = $nanoparticles.collect{|n| n if !n.coating[0].smiles.nil?}.compact.uniq + configure :development do #$logger = Logger.new(STDOUT) end @@ -18,7 +23,7 @@ get '/?' do end #=begin get '/qmrf-report/:id' do - prediction_model = Model::NanoPrediction.find(params[:id]) + prediction_model = OpenTox::Model::Validation.find(params[:id]) if prediction_model model = prediction_model.model model_type = "regression" @@ -74,24 +79,35 @@ end #=end get '/predict/?' do @prediction_models = [] - prediction_models = Model::NanoPrediction.all - prediction_models.each{|m| m.model[:algorithms]["descriptors"]["categories"] == ["P-CHEM"] ? @prediction_models[0] = m : @prediction_models[1] = m} - # define type (pc or pcp) - @prediction_models.each_with_index{|m,idx| idx == 0 ? m[:pc_model] = true : m[:pcp_model] = true} - # collect nanoparticles by training dataset (Ag + Au) - dataset = Dataset.find_by(:name=> "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles") - nanoparticles = dataset.nanoparticles + models = OpenTox::Model::Validation.all + prediction_models = models.delete_if{|m| m.model.name !~ /\b(Net cell association)\b/} + + # sort and collect prediction models + @prediction_models[0] = prediction_models.find{|m| m.model[:algorithms]["descriptors"]["method"] == "fingerprint"} + @prediction_models[1] = prediction_models.delete_if{|m| m.model[:algorithms]["descriptors"]["method"] == "fingerprint"}.find{|m| m.model[:algorithms]["descriptors"]["categories"][0] =~ /P-CHEM/} + @prediction_models[2] = prediction_models.find{|m| m.model[:algorithms]["descriptors"]["categories"][0] == "Proteomics"} + + # define type (fingerprint,physchem,proteomics) + @prediction_models[0]["type"] = "fingerprint" + @prediction_models[1]["type"] = "physchem" + @prediction_models[2]["type"] = "proteomics" + + # select relevant features for each model + @fingerprint_relevant_features = @prediction_models[0].model.substance_ids.collect{|id| Substance.find(id)} + fingerprint = $coating_list.sample + fingerprint.properties.delete_if{|id,v| !@fingerprint_relevant_features.include?(Feature.find(id))} + @example_fingerprint = fingerprint - # select physchem_parameters by relevant features for each model - @pc_relevant_features = @prediction_models[0].model.descriptor_ids.collect{|id, v| Feature.find(id)} - @pcp_relevant_features = @prediction_models[1].model.descriptor_ids.collect{|id, v| Feature.find(id)} - pcp = nanoparticles.sample - pcp.properties.delete_if{|id,v| !@pcp_relevant_features.include?(Feature.find(id))} - @example_pcp = pcp + @physchem_relevant_features = @prediction_models[1].model.descriptor_ids.collect{|id, v| Feature.find(id)} + physchem = $nanoparticles.sample + physchem.properties.delete_if{|id,v| !@physchem_relevant_features.include?(Feature.find(id))} + @example_physchem = physchem + + @proteomics_relevant_features = @prediction_models[2].model.descriptor_ids.collect{|id, v| Feature.find(id)} + proteomics = $nanoparticles.sample + proteomics.properties.delete_if{|id,v| !@proteomics_relevant_features.include?(Feature.find(id))} + @example_proteomics = proteomics - pc = nanoparticles.sample - pc.properties.delete_if{|id,v| !@pc_relevant_features.include?(Feature.find(id))} - @example_pc = pc haml :predict end @@ -102,50 +118,69 @@ get '/license' do end post '/predict/?' do - # choose the right prediction model - prediction_model = Model::NanoPrediction.find(params[:prediction_model]) + # select the prediction model + prediction_model = OpenTox::Model::Validation.find(params[:prediction_model]) size = params[:size].to_i @type = params[:type] - example_core = eval(params[:example_core]) - example_coating = eval(params[:example_coating]) + example_core = params[:example_core] + example_coating = params[:example_coating] example_pc = eval(params[:example_pc]) - - in_core = eval(params[:in_core]) - in_core["name"] = params[:input_core] - input_core = in_core - - in_coating = eval(params[:in_coating]) - in_coating[0]["name"] = params[:input_coating] - input_coating = in_coating + + input_core = params[:input_core] + input_coating = params[:input_coating] input_pc = {} - (1..size).each{|i| input_pc["#{params["input_key_#{i}"]}"] = [params["input_value_#{i}"].to_f] unless params["input_value_#{i}"] == "-"} - + if @type =~ /physchem|proteomics/ + (1..size).each{|i| input_pc["#{params["input_key_#{i}"]}"] = [params["input_value_#{i}"].to_f] unless params["input_value_#{i}"] == ""} + end # define relevant_features by input - @type = "pc" ? (@pc_relevant_features = input_pc.collect{|id,v| Feature.find(id)}) : (@pc_relevant_features = []) - @type = "pcp" ? (@pcp_relevant_features = input_pc.collect{|id,v| Feature.find(id)}) : (@pcp_relevant_features = []) - - if input_pc == example_pc && input_core == example_core && input_coating == example_coating - # unchanged input = database hit - nanoparticle = Nanoparticle.find_by(:id => params[:example_id]) - nanoparticle.properties = input_pc - @match = true - @nanoparticle = nanoparticle - @name = nanoparticle.name - else - # changed input = create nanoparticle to predict - nanoparticle = Nanoparticle.new - nanoparticle.core = input_core - nanoparticle.coating = input_coating - nanoparticle.properties = input_pc - @match = false - @nanoparticle = nanoparticle + (@type == "fingerprint") ? (@fingerprint_relevant_features = input_pc.collect{|id,v| Feature.find(id)}) : (@physchem_relevant_features = []) + (@type == "physchem") ? (@physchem_relevant_features = input_pc.collect{|id,v| Feature.find(id)}) : (@physchem_relevant_features = []) + (@type == "proteomics") ? (@proteomics_relevant_features = input_pc.collect{|id,v| Feature.find(id)}) : (@proteomics_relevant_features = []) + + + if @type =~ /physchem|proteomics/ + if input_pc == example_pc && input_core == example_core && input_coating == example_coating + # unchanged input = database hit + nanoparticle = Nanoparticle.find_by(:id => params[:example_id]) + nanoparticle.properties = input_pc + @match = true + @nanoparticle = nanoparticle + @name = nanoparticle.name + else + # changed input = create nanoparticle to predict + nanoparticle = Nanoparticle.new + nanoparticle.core_id = Compound.find_by(:name=>input_core).id.to_s + nanoparticle.coating_ids = [Compound.find_by(:name=>input_coating).id.to_s] + nanoparticle.properties = input_pc + @match = false + @nanoparticle = nanoparticle + end + end + + if @type == "fingerprint" + if input_core == example_core && input_coating == example_coating + # unchanged input = database hit + nanoparticle = Nanoparticle.find_by(:id => params[:example_id]) + #nanoparticle.properties = input_pc + @match = true + @nanoparticle = nanoparticle + @name = nanoparticle.name + else + # changed input = create nanoparticle to predict + nanoparticle = Nanoparticle.new + nanoparticle.core_id = Compound.find_by(:name=>input_core).id.to_s + nanoparticle.coating_ids = [Compound.find_by(:name=>input_coating).id.to_s] + @match = false + @nanoparticle = nanoparticle + end end + + # prediction output @input = input_pc @prediction = prediction_model.model.predict nanoparticle - haml :prediction end |