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-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | FAQ.md | 39 | ||||
-rw-r--r-- | Gemfile | 4 | ||||
-rw-r--r-- | LICENSE.md | 596 | ||||
-rw-r--r-- | VERSION | 2 | ||||
-rw-r--r-- | application.rb | 253 | ||||
-rw-r--r-- | config.ru | 3 | ||||
-rw-r--r-- | helper.rb | 215 | ||||
-rw-r--r-- | lazar-gui.gemspec | 14 | ||||
-rw-r--r-- | views/batch.haml | 106 | ||||
-rw-r--r-- | views/details.haml | 8 | ||||
-rw-r--r-- | views/faq_layout.haml | 67 | ||||
-rw-r--r-- | views/layout.haml | 43 | ||||
-rw-r--r-- | views/license.haml | 1 | ||||
-rw-r--r-- | views/model_details.haml | 158 | ||||
-rw-r--r-- | views/neighbors.haml | 24 | ||||
-rw-r--r-- | views/predict.haml | 13 | ||||
-rw-r--r-- | views/prediction.haml | 109 | ||||
-rw-r--r-- | views/style.scss | 14 | ||||
-rw-r--r-- | views/validation.haml | 16 |
20 files changed, 970 insertions, 716 deletions
@@ -1,3 +1,2 @@ Gemfile.lock .sass-cache/ -tmp/* @@ -1,29 +1,18 @@ -Frequently Asked Questions -========================== -<br> -####How does this prediction works? -> +## lazar Frequently Asked Questions -####You talk about significant fragments. Where can I find them? -> We will show up those significant fragments in a further version. +####The LAZAR program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version, I would consider a confidence value higher than 0.025 as reliable. But now, there is no such parameter in the prediction results. How can I consider a prediction as presenting high or low confidence? -####What is endpoint details about? -> You get the source from where we took compounds for the endpoint. The type and the number of compounds we used. +In the past many users had problems to interpret the confidence level, +for this reason we provide now the probabilities that the prediction +belongs to one of the two classes. In contrast to the confidence level, +these numbers can be interpreted as real probabilities ranging from 0 to +1. -####What is three times independent validation about? -> +Reliable prediction have a high probability for the predicted class and +a low probability for the other one. Unreliable predictions have similar +values for both classes, and are caused by a lot of contradictory +activities of similar compounds. -####Do you consider providing plots for the validation results? -> In a further version we will show up confidence and correlation plots. - -####What does 'Not enough similar compounds in training dataset' mean? -> Lazar uses neighbors from the training dataset of the endpoint to predict your compound. If there are not enough neighbors for Lazar it is not possible to make a prediction. - -####Is there a minimum number of necessary neighbors to make a prediction? -> - -####How can I activate the 'batch prediction' option? -> Please contact us directly via [mail](mailto:support@in-silico.ch). - -####Not the right answers for me. Is there a way to contact you or report problems. -> You can always ask your questions via [mail](mailto:support@in-silico.ch). If you run into problems with the GUI please post your issue [here](https://github.com/opentox/lazar-gui/issues). If you would like to post any other issue e.g. about an expected prediction result please use this [form](https://github.com/opentox/lazar/issues). +Probabilities are calculated from the activities and similarities of +neighbors, please make sure to inspect the neighbors list for any +inconsistencies that might affect the prediction. @@ -1,7 +1,9 @@ source "https://rubygems.org" gemspec -gem "lazar" +gem "lazar", :path => "../lazar" gem "gem-path" gem "sinatra" +gem "sinatra-reloader" gem "haml" gem "sass" +gem "rdiscount" diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..16d89e0 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,596 @@ +GNU GENERAL PUBLIC LICENSE +========================== + +Version 3, 29 June 2007 + +Copyright © 2007 Free Software Foundation, Inc. <<http://fsf.org/>> + +Everyone is permitted to copy and distribute verbatim copies of this license +document, but changing it is not allowed. + +## Preamble + +The GNU General Public License is a free, copyleft license for software and other +kinds of works. + +The licenses for most software and other practical works are designed to take away +your freedom to share and change the works. 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Disclaimer of Warranty. + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. +EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER +EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE +QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +### 16. Limitation of Liability. + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY +COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS +PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, +INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE +PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE +OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE +WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16. + +If the disclaimer of warranty and limitation of liability provided above cannot be +given local legal effect according to their terms, reviewing courts shall apply local +law that most closely approximates an absolute waiver of all civil liability in +connection with the Program, unless a warranty or assumption of liability accompanies +a copy of the Program in return for a fee. + +END OF TERMS AND CONDITIONS + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest possible use to +the public, the best way to achieve this is to make it free software which everyone +can redistribute and change under these terms. + +To do so, attach the following notices to the program. It is safest to attach them +to the start of each source file to most effectively state the exclusion of warranty; +and each file should have at least the “copyright” line and a pointer to +where the full notice is found. + + <one line to give the program's name and a brief idea of what it does.> + Copyright (C) <year> <name of author> + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short notice like this +when it starts in an interactive mode: + + <program> Copyright (C) <year> <name of author> + This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type 'show c' for details. + +The hypothetical commands 'show w' and 'show c' should show the appropriate parts of +the General Public License. Of course, your program's commands might be different; +for a GUI interface, you would use an “about box”. + +You should also get your employer (if you work as a programmer) or school, if any, to +sign a “copyright disclaimer” for the program, if necessary. For more +information on this, and how to apply and follow the GNU GPL, see +<<http://www.gnu.org/licenses/>>. + +The GNU General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may consider it +more useful to permit linking proprietary applications with the library. If this is +what you want to do, use the GNU Lesser General Public License instead of this +License. But first, please read +<<http://www.gnu.org/philosophy/why-not-lgpl.html>>.
\ No newline at end of file @@ -1 +1 @@ -1.0.2 +1.1.1 diff --git a/application.rb b/application.rb index b9c267c..fa5df0a 100644 --- a/application.rb +++ b/application.rb @@ -1,11 +1,6 @@ #require_relative 'helper.rb' -#require 'rdiscount' +require 'rdiscount' include OpenTox -#require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb") # until added to ot-tools - -# DG: workaround for https://github.com/sinatra/sinatra/issues/808 -# Date: 18/11/2013 -#set :protection, :except => :path_traversal configure :development do $logger = Logger.new(STDOUT) @@ -20,230 +15,87 @@ helpers do end +before do + @version = File.read("VERSION").chomp +end + get '/?' do redirect to('/predict') end get '/predict/?' do - @version = File.read("VERSION").chomp - @models = OpenTox::Model::Prediction.all + @models = OpenTox::Model::Validation.all + @models = @models.delete_if{|m| m.model.name =~ /\b(Net cell association)\b/} @endpoints = @models.collect{|m| m.endpoint}.sort.uniq @models.count <= 0 ? (haml :info) : (haml :predict) end get '/predict/modeldetails/:model' do - model = OpenTox::Model::Prediction.find params[:model] - crossvalidations = model.crossvalidations - #confidence_plots = crossvalidations.collect{|cv| [cv.id, cv.confidence_plot]} - #confidence_plots.each do |confp| - # File.open(File.join('public', "confp#{confp[0]}.svg"), 'w'){|file| file.write(confp[1])} unless File.exists? File.join('public', "confp#{confp[0]}.svg") - #end - #if model.regression? - # correlation_plots = crossvalidations.collect{|cv| [cv.id, cv.correlation_plot]} - # correlation_plots.each do |corrp| - # File.open(File.join('public', "corrp#{corrp[0]}.svg"), 'w'){|file| file.write(corrp[1])} unless File.exists? File.join('public', "corrp#{corrp[0]}.svg") - # end - #end + model = OpenTox::Model::Validation.find params[:model] + crossvalidations = OpenTox::Validation::RepeatedCrossValidation.find(model.repeated_crossvalidation_id).crossvalidations - return haml :model_details, :layout=> false, :locals => {:model => model} -end - -get '/jme_help/?' do - File.read(File.join('views','jme_help.html')) + return haml :model_details, :layout=> false, :locals => {:model => model, :crossvalidations => crossvalidations} end # get individual compound details get '/prediction/:neighbor/details/?' do - @compound = OpenTox::Compound.new params[:neighbor] + @compound = OpenTox::Compound.find params[:neighbor] @smiles = @compound.smiles - task = OpenTox::Task.run("Get names for '#{@smiles}'.") do - names = @compound.names - end - task.wait - - case task[RDF::OT.hasStatus] - when "Error" - @names = "No names for this compound available." - when "Completed" - @names = @compound.names - else + begin + @names = @compound.names.nil? ? "No names for this compound available." : @compound.names + rescue @names = "No names for this compound available." end @inchi = @compound.inchi.gsub("InChI=", "") haml :details, :layout => false end -=begin -# sdf representation for datasets -#TODO fix 502 errors from compound service -get '/predict/:dataset_uri/sdf/?' do - uri = CGI.unescape(params[:dataset_uri]) - $logger.debug uri - bad_request_error "Not a dataset uri." unless URI.dataset? uri - dataset = OpenTox::Dataset.find uri - @compounds = dataset.compounds - @data_entries = dataset.data_entries - sum="" - @compounds.each_with_index{ |c, idx| - sum << c.inchi - sum << c.sdf.sub(/\n\$\$\$\$/,'') - @data_entries[idx].each{ |f,v| - sum << "> <\"#{f}\">\n" - sum << v.join(", ") - sum << "\n\n" - } - sum << "$$$$\n" - } - send_file sum, :filename => "#{dataset.title}.sdf" -end -=end -# fingerprints for compound in predictions -get '/prediction/:model_uri/:type/:compound_uri/fingerprints/?' do - @type = params[:type] - model = OpenTox::Model::Lazar.find params[:model_uri] - feature_dataset = OpenTox::Dataset.find model[RDF::OT.featureDataset] - @compound = OpenTox::Compound.new params[:compound_uri] - @significant_fragments = [] - if @type =~ /classification/i - # collect all feature values with fingerprint - fingerprints = OpenTox::Algorithm::Descriptor.send("smarts_match", [@compound], feature_dataset.features.collect{ |f| f[RDF::DC.title]})[@compound.uri] - #$logger.debug "fingerprints:\t#{fingerprints}\n" - - # collect fingerprints with value 1 - @fingerprint_values = fingerprints.collect{|smarts, value| [smarts, value] if value > 0} - - # collect all features from feature_dataset - @features = feature_dataset.features.collect{|f| f } - - # search for each fingerprint in all features and collect feature values( effect, smarts, pValue ) - @fingerprint_values.each{ |fi, v| @features.each{ |f| @significant_fragments << [f[RDF::OT.effect].to_i, f[RDF::OT.smarts], f[RDF::OT.pValue]] if fi == f[RDF::OT.smarts] } } - - # pass value_map, important to interprete effect value - prediction_feature_uri = "" - model.parameters.each {|p| - if p[RDF::DC.title].to_s == "prediction_feature_uri" - prediction_feature_uri = p[RDF::OT.paramValue].object - end - } - prediction_feature = OpenTox::Feature.find prediction_feature_uri - @value_map = prediction_feature.value_map - - else #regression - feature_calc_algo = "" - model.parameters.each {|p| - if p[RDF::DC.title].to_s == "feature_calculation_algorithm" - feature_calc_algo = p[RDF::OT.paramValue].object - end - } - - @desc = [] - fingerprints = OpenTox::Algorithm::Descriptor.send( feature_calc_algo, [ @compound ], feature_dataset.features.collect{ |f| f[RDF::DC.title] } ) - fingerprints.each{|x, h| h.each{|descriptor, value| @desc << [descriptor, [value]]}} - - pc_descriptor_titles_descriptions = {} - feature_dataset.features.collect{ |f| - pc_descriptor_titles_descriptions[f[RDF::DC.title]]= f[RDF::DC.description] - } - - @desc.each{|d, v| @significant_fragments << [pc_descriptor_titles_descriptions[d], v] } - end - haml :significant_fragments, :layout => false +get '/jme_help/?' do + File.read(File.join('views','jme_help.html')) end -get '/prediction/:model_uri/:type/:neighbor/significant_fragments/?' do - @type = params[:type] - @compound = OpenTox::Compound.new params[:neighbor] - model = OpenTox::Model::Lazar.find params[:model_uri] - #$logger.debug "model for significant fragments:\t#{model.uri}" - - feature_dataset = OpenTox::Dataset.find model[RDF::OT.featureDataset] - $logger.debug "feature_dataset_uri:\t#{feature_dataset.uri}\n" - - # load all compounds - feature_dataset.compounds - - # load all features - @features = feature_dataset.features.collect{|f| f} - - # find all features and values for a neighbor compound - @significant_fragments = [] - # check type first - if @type =~ /classification/i - # get compound index in feature dataset - c_idx = feature_dataset.compound_indices @compound.uri - - # collect feature uris with value - @feat = @features.collect{|f| [feature_dataset.data_entry_value(c_idx[0], f.uri), f.uri]} - #$logger.debug "@feat:\t#{@feat}\n" - - # pass feature uris if value > 0 - @feat.each do |f| - # search relevant features - if f[0] > 0 - f = OpenTox::Feature.find f[1] - # pass relevant features with [ effect, smarts, pValue ] - @significant_fragments << [f[RDF::OT.effect].to_i, f[RDF::OT.smarts], f[RDF::OT.pValue].to_f.round(3)] - end - end - # pass value_map, important to interprete effect value - prediction_feature_uri = "" - model.parameters.each {|p| - if p[RDF::DC.title].to_s == "prediction_feature_uri" - prediction_feature_uri = p[RDF::OT.paramValue].object - end - } - prediction_feature = OpenTox::Feature.find prediction_feature_uri - @value_map = prediction_feature.value_map - - else # regression - # find a value in feature dataset by compound and feature - @values = @features.collect{|f| feature_dataset.values(@compound, f)} - #$logger.debug "values in fd:\t#{@values}" - - @features.each_with_index{|f, i| @significant_fragments << [f.description, @values[i]]} - end - #$logger.debug "significant fragments:\t#{@significant_fragments}\n" - - haml :significant_fragments, :layout => false +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/?:csv?' do response['Content-Type'] = "text/csv" - @csv = "\"Compound\",\"Endpoint\",\"Type\",\"Prediction\",\"Confidence\"\n" + @csv = "\"Compound\",\"Endpoint\",\"Type\",\"Prediction\",\"95% Prediction interval\"\n" @@batch.each do |key, values| + compound = key + smiles = compound.smiles values.each do |array| model = array[0] + type = model.model.class.to_s.match("Classification") ? "Classification" : "Regression" prediction = array[1] - compound = key.smiles - mw = key.molecular_weight endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" if prediction[:confidence] == "measured" if prediction[:value].is_a?(Array) prediction[:value].each do |value| - type = "" - weight = Compound.from_smiles(compound).mmol_to_mg(value, mw) - pred = value.numeric? ? "#{'%.2e' % value} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : value - confidence = "measured activity" - @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n" + pred = value.numeric? ? "#{value} (#{model.unit}), #{compound.mmol_to_mg(value.delog10)} #{(model.unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : value + int = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval]) + interval = (int.nil? ? "--" : "#{int[1].delog10} - #{int[0].delog10} (#{model.unit})") + @csv += "\"#{smiles}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{interval}\"\n" end else - type = "" - weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw) - pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value] + pred = prediction[:value].numeric? ? "#{prediction[:value]} (#{model.unit}), #{compound.mmol_to_mg(prediction[:value].delog10)} #{(model.unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] confidence = "measured activity" end elsif prediction[:neighbors].size > 0 - weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw) type = model.model.class.to_s.match("Classification") ? "Classification" : "Regression" - pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value] - confidence = prediction[:confidence] + pred = prediction[:value].numeric? ? "#{prediction[:value].delog10} (#{model.unit}), #{compound.mmol_to_mg(prediction[:value].delog10)} #{(model.unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] + int = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval]) + interval = (int.nil? ? "--" : "#{int[1].delog10} - #{int[0].delog10} (#{model.unit})") else type = "" pred = "Not enough similar compounds in training dataset." - confidence = "" + interval = "" end - @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n" unless prediction[:value].is_a?(Array) + @csv += "\"#{smiles}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{interval}\"\n" unless prediction[:value].is_a?(Array) end end @csv @@ -261,11 +113,21 @@ post '/predict/?' do f.write(params[:fileselect][:tempfile].read) end @filename = params[:fileselect][:filename] - input = OpenTox::Dataset.from_csv_file File.join "tmp", params[:fileselect][:filename] - dataset = OpenTox::Dataset.find input.id + begin + input = OpenTox::Dataset.from_csv_file File.join("tmp", params[:fileselect][:filename]), true + if input.class == OpenTox::Dataset + dataset = OpenTox::Dataset.find input + else + @error_report = "Could not serialize file '#{@filename}' ." + return haml :error + end + rescue + @error_report = "Could not serialize file '#{@filename}' ." + return haml :error + end @compounds = dataset.compounds if @compounds.size == 0 - @error_report = "No valid SMILES submitted." + @error_report = dataset[:warnings] dataset.delete return haml :error end @@ -273,13 +135,15 @@ post '/predict/?' do @compounds.each do |compound| @batch[compound] = [] params[:selection].keys.each do |model_id| - model = Model::Prediction.find model_id + model = OpenTox::Model::Validation.find model_id prediction = model.predict(compound) @batch[compound] << [model, prediction] end end @@batch = @batch + @warnings = dataset[:warnings] dataset.delete + File.delete File.join("tmp", params[:fileselect][:filename]) return haml :batch end @@ -291,26 +155,31 @@ post '/predict/?' do # get compound from SMILES @compound = Compound.from_smiles @identifier if @compound.blank? - @error_report = "Attention, '#{@identifier}' is not a valid SMILES string." + @error_report = "'#{@identifier}' is not a valid SMILES string." return haml :error end @models = [] @predictions = [] params[:selection].keys.each do |model_id| - model = Model::Prediction.find model_id + model = OpenTox::Model::Validation.find model_id @models << model @predictions << model.predict(@compound) end haml :prediction end end -=begin + +get '/license' do + @license = RDiscount.new(File.read("LICENSE.md")).to_html + haml :license, :layout => false +end + get '/faq' do @faq = RDiscount.new(File.read("FAQ.md")).to_html - haml :faq, :layout => :faq_layout + haml :faq, :layout => false end -=end + get '/style.css' do headers 'Content-Type' => 'text/css; charset=utf-8' scss :style @@ -1,5 +1,6 @@ -SERVICE = "lazar" +ENV["LAZAR_ENV"] = "development"#"production" require 'bundler' Bundler.require require File.expand_path './application.rb' +require "sinatra/reloader" if development? run Sinatra::Application @@ -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 diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index af5f0f9..f37b512 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -13,13 +13,13 @@ Gem::Specification.new do |s| s.rubyforge_project = "lazar-gui" s.files = `git ls-files`.split("\n") - s.add_runtime_dependency "lazar", "~> 0.9.3", '>= 0.9.3' - s.add_runtime_dependency "gem-path", "~> 0.6.1", '>= 0.6.1' - s.add_runtime_dependency "sinatra", "~> 1.4.0", '>= 1.4.0' - s.add_runtime_dependency "rdiscount", "~> 2.1.0", '>= 2.1.0' - s.add_runtime_dependency "haml", "~> 4.0.0", '>= 4.0.0' - s.add_runtime_dependency "sass", "~> 3.4.0", '>= 3.4.0' - s.add_runtime_dependency "unicorn", "~> 5.1.0", '>= 5.1.0' + s.add_runtime_dependency "lazar", "= 1.0.0" + s.add_runtime_dependency "gem-path" + s.add_runtime_dependency "sinatra" + s.add_runtime_dependency "rdiscount" + s.add_runtime_dependency "haml" + s.add_runtime_dependency "sass" + s.add_runtime_dependency "unicorn" s.post_install_message = %q{ Service cmds: diff --git a/views/batch.haml b/views/batch.haml index 9bfa67e..6c37a2b 100644 --- a/views/batch.haml +++ b/views/batch.haml @@ -2,57 +2,99 @@ %a.btn.btn-warning{:href => to('/predict')} %span.glyphicon.glyphicon-menu-left{:aria=>{:hidden=>"true"}} New Prediction - / displays all prediction result in first table + %a.btn.btn-success{:href=>"#{to("/predict/#{@filename}")}", :title=>"download"} + %span.glyphicon.glyphicon-download-alt + download CSV + + / show processed file name + %topline + %div.row + %div.col-md-4 + %h3 Batch Prediction Results: + %div.col-md-8 + %h3= @filename + + / displays all prediction result in one table %div.table-responsive %table.table.table-bordered{:id=>"batch", :style=>"background-color:white;"} - %thead - %tr - %h3.col-md-4{:style=>"padding-left:0;"} Batch Prediction Results: - %h3.col-md-8= @filename - %tr - %span.btn.btn-default - %a{:href=>"#{to("/predict/#{@filename}")}", :title=>"download"} - %span.glyphicon.glyphicon-download-alt{:aria=>{:hidden=>"true"}} - CSV %tbody - / key = compound, values = array of arrays with model, prediction + - if @warnings + - @warnings.each do |warning| + %tr + %td + %b Warning + %td + = warning.sub(/\b(tmp\/)\b/,"") + / key = compound, values = [model,prediction] - @batch.each do |key, values| - compound = key - - mw = compound.molecular_weight %tr %td{:style=>"vertical-align:top;"} %p= compound.svg %p= compound.smiles - / array = single prediction [endpoint, result] + + / array[0] = model, array[1] = prediction - values.each_with_index do |array,i| %td{:style=>"vertical-align:top;white-space:nowrap;"} - model = array[0] + / model type (classification|regression) + - model.model.class.to_s.match("Classification") ? type = "Classification" : type = "Regression" + - unit = model.unit - prediction = array[1] + %b{:class => "title"} = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" - %p - - if prediction[:confidence] == "measured" + + / check for prediction + - if prediction[:neighbors].size > 0 %p - %b Measured activity: - - if prediction[:value].is_a?(Array) - = prediction[:value][0].numeric? ? prediction[:value].collect{|v| weight = compound.mmol_to_mg(v, mw); '%.2e' % v + " (#{model.unit})"+" | #{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ") - - else - = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] + / show model type (classification|regression) + %b Type: + = type %p - %b Compound is part of the training dataset - - elsif prediction[:neighbors].size > 0 + / check for database hit + - if prediction[:warning] =~ /\b(identical)\b/i + + / show message about dbhit and measurements + %p + %b Compound is part of the training dataset + %p + %b Measured activity: + %br + - if prediction[:measurements].is_a?(Array) + = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10} (#{unit})</br>#{compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ") + - else + = (type == "Regression") ? "#{prediction[:measurements].delog10} (#{unit})</br>#{compound.mmol_to_mg(prediction[:measurements].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements] + + + / show prediction %p - / model type (classification|regression) - %b Type: - = model.model.class.to_s.match("Classification") ? "Classification" : "Regression" - %br - %b Prediction: - = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] - %br - / TODO probability - %b Confidence: - = prediction[:confidence].round(3) + %b Prediction: + %br + = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] + + / show prediction interval or probability + %p + - if type == "Regression" + %b 95% Prediction interval: + - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval]) + %br + = interval.nil? ? "--" : "#{interval[1].delog10} - #{interval[0].delog10} (#{unit})" + %br + = "#{compound.mmol_to_mg(interval[1].delog10)} - #{compound.mmol_to_mg(interval[0].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil? + - else + %b Probability: + - unless prediction[:probabilities].nil? + %br + = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}" + %br + / show warnings %p + - if !prediction[:warning].nil? + %b Warnings: + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"#{prediction[:warning]}"}} + + / no prediction - else %p = "Not enough similar compounds </br>in training dataset." diff --git a/views/details.haml b/views/details.haml index 8a57440..be4948a 100644 --- a/views/details.haml +++ b/views/details.haml @@ -1,8 +1,12 @@ +:javascript + $(document).ready(function(){ + addExternalLinks(); + }); %div.modal-body{:style=>"padding:10px;"} %button.close{ :type=>" button", data: { dismiss:"modal"}} × %h3 Names and synonyms: - %img.img-responsive{:src=>"#{@compound.uri}/image", :alt=>"Compound image not available", :width=>"300px", :heigth=>"300px", :style=>"float:left;"} + %p= @compound.svg %p %b="SMILES:" %p= @smiles @@ -19,6 +23,6 @@ %hr %p{:style=>"padding-left:0.5em;"} / pubchem link - %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :target=>"_blank"} PubChem read across + %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :rel=>"external"} PubChem read across %i (experimental) %br diff --git a/views/faq_layout.haml b/views/faq_layout.haml deleted file mode 100644 index a9b6664..0000000 --- a/views/faq_layout.haml +++ /dev/null @@ -1,67 +0,0 @@ -!!! -%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"} - %head - %meta{'charset'=>"utf-8"} - %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"} - %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"} - %title Lazar GUI FAQ - %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'} - %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"} - %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"} - %link{:rel=>'stylesheet', :href=>"#{'/css/theme.bootstrap.min.css'}"} - %link{ :href=>"/style.css", :rel=>"stylesheet"} - %link{ :href=>"/stylesheets/jquery-ui.css", :rel=>"stylesheet"} - %script{:src=>"/javascripts/jquery-1.11.2.min.js"} - %script{:src=>"/javascripts/bootstrap.min.js"} - %script{ :src=>"/javascripts/lazar-gui.js"} - %body - %noscript - %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"} - Your web browser must have JavaScript enabled in order for this application to display correctly. - %header.page-header - %div.row - %div.col-md-2 - %a{:href=> to("/predict")} - %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"} - %div.col-md-10 - %h1.media-heading{:style=>"margin: 0 0 0 1em;display:inline;"} Lazar GUI - A Graphical User Interface for the <a href="http://github.com/opentox/lazar">Lazar</a> framework - - %div.container-fluid - :javascript - $(document).ready(function(){ - $("#back-top").hide(); - $(".blind").error(function(){ - $(this).attr('src', '/images/blind.png'); - }); - }); - - = yield - - %footer.footer - %div.container-fluid - %p.text-muted - © - %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s} - - #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"} - %a{:href => "", :style=>"text:decoration:none;color:#ccc;"} - %span.glyphicon.glyphicon-circle-arrow-up{:style => "font-size:3em;color:black;"} - :javascript - $("#back-top").hide(); - $(function () { - $(window).scroll(function () { - if ($(this).scrollTop() > 600) { - $('#back-top').fadeIn(); - } else { - $('#back-top').fadeOut(); - } - }); - // scroll body to 0px on click - $('#back-top a').click(function () { - $('body,html').animate({ - scrollTop: 0 - }, 500); - return false; - }); - }); diff --git a/views/layout.haml b/views/layout.haml index 5d6d57a..8a920ea 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -15,7 +15,7 @@ %script{:src=>"/javascripts/bootstrap.min.js"} %script{:src=>"/javascripts/jquery.tablesorter.min.js"} %script{:src=>"/javascripts/jquery.tablesorter.widgets.js"} - %script{ :src=>"/javascripts/lazar-gui.js"} + %script{:src=>"/javascripts/lazar-gui.js"} %body %noscript %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"} @@ -26,34 +26,35 @@ %a{:href=> to("/predict")} %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"150px", :heigth=>"150px", :style=>"margin:0 3em 0 2em;"} %div.col-md-8 - %h1.media-heading{:style=>"margin: 0 0 0 2em;"} + %h1.media-heading lazar toxicity predictions %div.col-md-2 %h1.media-heading %small - %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar + %a{:href=>"https://nano-lazar.in-silico.ch", :rel=>"external"} nano-lazar %div.container-fluid %topline %div.row - %div.col-md-8 + %div.col-md-10 Problems, bugs, ideas for improvements ? Please report at our %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker - or send us an email - %a{ :href=>"mailto:info@in-silico.ch", :target=>"_top"} + , check out the + %a{:href=> to("/faq"), :rel => "external"} FAQ + page or send us an email. + %a{ :href=>"mailto:info@in-silico.ch?subject=[lazar v#{@version}]", :target=>"_top"} %img.share{:src=>"/images/Email.png"} - (version #{@version}). - %div.col-md-2 - %div.col-md-2 - %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"} + [version: #{@version}] + %div.col-md-2{:style=>"text-align:right;"} + %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Tweet"} %img.share{:src=>"/images/Twitter.png"} - %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"} + %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Google+"} %img.share{:src=>"/images/Google+.png"} - %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"} + %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on LinkedIn"} %img.share{:src=>"/images/LinkedIn.png"} - %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Facebook"} + %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Facebook"} %img.share{:src=>"/images/Facebook.png"} - + :javascript $(document).ready(function(){ $("#back-top").hide(); @@ -77,17 +78,19 @@ %p.text-muted © %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s} + | + %a{:href => to("/license"), :rel => "external"} GPL3 License %supporters.col-md-12 - %p Financial support: - %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"} + %p Financial support by + %a{:href=>"http://www.bfr.bund.de/de/start.html", :rel=>"external"} %img{:src=>"/images/bfr_logo.gif"} - %a{:href=>"http://www.opentox.org/", :target=>"_blank"} + %a{:href=>"http://www.opentox.org/", :rel=>"external"} %img{:src=>"/images/ot_logo.png"} - %a{:href=>"https://enanomapper.net/", :target=>"_blank"} + %a{:href=>"https://enanomapper.net/", :rel=>"external"} %img{:src=>"/images/enm_logo.png"} - %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"} + %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :rel=>"external"} %img{:src=>"/images/nestec.jpg"} - + #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"} %a{:href => "", :style=>"text:decoration:none;color:#ccc;"} diff --git a/views/license.haml b/views/license.haml new file mode 100644 index 0000000..2813220 --- /dev/null +++ b/views/license.haml @@ -0,0 +1 @@ += @license diff --git a/views/model_details.haml b/views/model_details.haml index 1be75e7..5c3aa4f 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -1,26 +1,43 @@ %b Model: %br Source: -%a{:href=>model.source, :target=>"external"} +%a{:href=>model.source, :rel=>"external"} = model.source %br - model.classification? ? type = "Classification" : type = "Regression" = "Type:\t" = type %br -- training_dataset = OpenTox::Dataset.find model.training_dataset.id +- training_dataset = OpenTox::Dataset.find model.model.training_dataset_id = "Training compounds:\t" -= training_dataset.compounds.size - += training_dataset.data_entries.size +%br += "Training dataset:\t" +%a{:href=>"#{to("/predict/dataset/#{training_dataset.name}")}"} + = training_dataset.name +%br +%b Algorithms: +%br +Similarity: +%a{:href=> "http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["similarity"]["method"].sub("::", "%2F")}", :rel=>"external"} + = model.model.algorithms["similarity"]["method"] += ", min: #{model.model.algorithms["similarity"]["min"]}" +%br +Prediction: +%a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"} + = model.model.algorithms["prediction"]["method"] +%br +Descriptors: += model.model.algorithms["descriptors"]["method"]+"," += model.model.algorithms["descriptors"]["type"] %p - if type == "Classification" %b Independent crossvalidations: - else %b Independent crossvalidations (-log10 transformed): %div.row{:id=>"validations#{model.id}", :style=>"background-color:#f5f5f5;"} - - model.crossvalidations.each do |crossvalidation| + - crossvalidations.each do |cv| %span.col-xs-4.col-sm-4.col-md-4.col-lg-4 - - cv = OpenTox::CrossValidation.find crossvalidation.id = "Num folds:\t" = cv.folds %br @@ -34,76 +51,83 @@ Source: = "Accuracy:\t" = cv.accuracy.round(3) if cv.accuracy %br - = "True positive rate:\t" - = cv.true_rate["active"].round(3) if cv.true_rate["active"] - %br - = "True negative rate:\t" - = cv.true_rate["inactive"].round(3) if cv.true_rate["inactive"] - %br - = "Positive predictive value:\t" - = cv.predictivity["active"].round(3) if cv.predictivity["active"] - %br - = "Negative predictive value:\t" - = cv.predictivity["inactive"].round(3) if cv.predictivity["inactive"] + = "Weighted accuracy:\t" + = cv.weighted_accuracy.round(3) if cv.weighted_accuracy + - if cv.true_rate + %br + = "True positive rate:\t" + = cv.true_rate[cv.accept_values[0]].round(3) + %br + = "True negative rate:\t" + = cv.true_rate[cv.accept_values[1]].round(3) + - if cv.predictivity + %br + = "Positive predictive value:\t" + = cv.predictivity[cv.accept_values[0]].round(3) + %br + = "Negative predictive value:\t" + = cv.predictivity[cv.accept_values[1]].round(3) %p - %b Confusion Matrix: - %table.table.table-condensed.table-borderless{:style=>"width:20%;"} - %tbody - %tr - %td - %td - %td - %b actual - %td - %td - %tr - %td - %td - %td active - %td inactive - -#%td total - %tr - %td - %b predicted - %td active - %td - =cv.confusion_matrix[0][0] - %td - =cv.confusion_matrix[0][1] - -#%td - =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1] - %tr - %td - %td inactive - %td - =cv.confusion_matrix[1][0] - %td - =cv.confusion_matrix[1][1] - -#%td - =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1] - -#%tr - %td - %td total - %td - =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0] - %td - =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1] - %td - -#= "Confusion Matrix:\t" - -#= cv.confusion_matrix + - ["confusion_matrix", "weighted_confusion_matrix"].each_with_index do |matrix,idx| + %b= (idx == 0 ? "Confusion Matrix" : "Weighted Confusion Matrix") + %table.table.table-condensed.table-borderless{:style=>"width:20%;"} + %tbody + %tr + %td + %td + %td + %b actual + %td + %td + %tr + %td + %td + %td active + %td inactive + -#%td total + %tr + %td + %b predicted + %td active + %td + =( idx == 1 ? cv.send(matrix)[0][0].round(3) : cv.send(matrix)[0][0]) + %td + =( idx == 1 ? cv.send(matrix)[0][1].round(3) : cv.send(matrix)[0][1]) + -#%td + =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1] + %tr + %td + %td inactive + %td + =( idx == 1 ? cv.send(matrix)[1][0].round(3) : cv.send(matrix)[1][0]) + %td + =( idx == 1 ? cv.send(matrix)[1][1].round(3) : cv.send(matrix)[1][1]) + -#%td + =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1] + -#%tr + %td + %td total + %td + =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0] + %td + =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1] + %td + -#= "Confusion Matrix:\t" + -#= cv.confusion_matrix + %br %br /= "Confidence plot:" /%p.plot / %img{:src=>"confp#{cv.id}.svg"} - if model.regression? %br - = "Root mean squared error:\t" + %a.ht5{:href=>"https://en.wikipedia.org/wiki/Root-mean-square_deviation", :rel=>"external"} RMSE: = cv.rmse.round(3) if cv.rmse %br - = "Mean absolute error:\t" + %a.ht5{:href=>"https://en.wikipedia.org/wiki/Mean_absolute_error", :rel=>"external"} MAE: = cv.mae.round(3) if cv.mae %br - = "R square:\t" + %a.ht5{:href=>"https://en.wikipedia.org/wiki/Coefficient_of_determination", :rel=>"external"}= "R"+"<sup>2</sup>"+":" = cv.r_squared.round(3) if cv.r_squared %br /= "Confidence plot:" @@ -113,5 +137,5 @@ Source: /= "Correlation plot" /%p.plot / %img{:src=>"/corrp#{cv.id}.svg"} - -%br + +%br diff --git a/views/neighbors.haml b/views/neighbors.haml index 096e432..2d7c4a5 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -67,10 +67,10 @@ Compound %th.sorter-false{:style =>"vertical-align:middle;"} Measured Activity - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"} + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"} %th.sorter-false{:style =>"vertical-align:middle;"} Similarity - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"} + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"<a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"} / %th{:style =>"vertical-align:middle;"} / Supporting Information %tbody @@ -79,20 +79,22 @@ - prediction[:neighbors].uniq.each_with_index do |neighbor,count| %tr / Compound - - c = Compound.find(neighbor["_id"]) + - c = Compound.find(neighbor) %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"} - /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor["_id"])}/details"), :id=>"link#{j+1}#{count}"}} - %p= c.svg + %a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(c.id.to_s)}/details"), :id=>"link#{j+1}#{count}"}} + = c.svg %p= c.smiles - - mw = c.molecular_weight - / Measured Activity = compound.features + + / Measured Activity %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"} - - features = c.features.collect{|k,v| v if k == predictionFeature[j]["id"] }.compact.flatten - = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" , #{'%.2e' % weight} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : features.join("</br>") + - if neighbor[:measurement].is_a?(Array) + = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : neighbor[:measurement].join(", ") + - else + = (type == "Regression") ? "#{neighbor[:measurement].delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(neighbor[:measurement].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement] + / Similarity = tanimoto %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"} - / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset? - = neighbor[:tanimoto] != nil ? neighbor[:tanimoto].to_f.round(3) : "Not enough similar compounds </br>in training dataset." + = neighbor[:similarity].round(3) - else %span.btn.btn-default.disabled diff --git a/views/predict.haml b/views/predict.haml index 010ed12..59630d0 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -111,7 +111,7 @@ }; // whole site content needs to be in one form. Input and checkboxes are proofed by js functions. -%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return !!(showcircle())" } +%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return !!(showcircle())" } %fieldset#top.well %h2 1. Draw a chemical structure #insert @@ -125,11 +125,13 @@ %br %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'} %p - %label{:for=>"fileselect"} + -#%label{:for=>"fileselect"} or upload a CSV file for batch predictions (disabled in public version) - %br - %span.btn.btn-default.btn-file - %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"} + -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}} + -#%br + -#%span.btn.btn-default.btn-file + -#%input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"} + %input{:type=>"hidden", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"} %fieldset#middle.well %h2 2. Select one or more endpoints @@ -162,6 +164,7 @@ document.getElementById("details#{model.id}").appendChild(details); $(button).show(); $(image).hide(); + addExternalLinks(); }); } } diff --git a/views/prediction.haml b/views/prediction.haml index 0f3d57b..1b8d38d 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -1,10 +1,3 @@ -:javascript - $(document).ready(function(){ - $('[data-toggle="popover"]').popover(); - $('.modal').on('hidden.bs.modal', function () { - $(this).removeData('bs.modal'); - }); - }); %div.well %a.btn.btn-warning{:href => to('/predict')} %i.glyphicon.glyphicon-menu-left @@ -16,9 +9,9 @@ %tbody %tr %td{:id=>"compound", :style=>"vertical-align:top;"} - %p= @compound.svg + %a.btn.btn-link{:href => "#details0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@compound.id.to_s)}/details"), :id=>"link01"}} + = @compound.svg %p= @compound.smiles - - mw = @compound.molecular_weight - @model_types = {} - @dbhit = {} - @predictions.each_with_index do |prediction,i| @@ -28,52 +21,66 @@ %td{:style=>"vertical-align:top;white-space:nowrap;"} %b{:class => "title"} = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})" - %p - - if prediction[:confidence] == "measured" - - @dbhit[i] = true + + / check for prediction + - if prediction[:neighbors].size > 0 %p - %b Measured activity: - - p prediction[:value] - - if prediction[:value].is_a?(Array) - = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{unit})"+", #{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ") - - else - = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] - %p - %b Compound is part of the training dataset - - elsif prediction[:neighbors].size > 0 - %p - / model type (classification|regression) + / show model type (classification|regression) %b Type: = type - %br - %b Prediction: - = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) , #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] - / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF. - / prediction popover - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}} - %br - - if type == "Regression" - %b 95% Prediction interval: - - interval = prediction[:prediction_interval].nil? ? " - - " : prediction[:prediction_interval].collect{|i| i.round(2)} - %br - = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" - / prediction intervall popover - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}} + %p + / check for database hit + - if prediction[:warning] =~ /\b(identical)\b/i + - @dbhit[i] = true + + / show message about dbhit and measurements + %p + %b Compound is part of the training dataset + %p + %b Measured activity: + %br + - if prediction[:measurements].is_a?(Array) + = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ") + - else + = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements] + - else - %b Confidence: - = prediction[:confidence].round(2) unless prediction[:confidence].nil? - / confidence popover - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}} + - @dbhit[i] = false + + / show prediction %p - /TODO add tooltip for significant ftagments and descriptors - / - if @model_type[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) - / Significant fragments: - / %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments - / - if @model_type[i] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) - / Descriptors - / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors - / %p + %b Prediction: + / prediction popover + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}} + %br + = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] + + / show prediction interval or probability + %p + - if type == "Regression" + %b 95% Prediction interval: + - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval]) + / prediction interval popover + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}} + %br + = interval.nil? ? "--" : "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)} (#{unit})" + %br + = "#{@compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{@compound.mmol_to_mg(interval[0].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil? + - else + %b Probability: + / probability popover + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Pobability", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Probability that the prediction belongs to one of the given classes."}} + - unless prediction[:probabilities].nil? + %br + = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0].signif(3)}" + %br + = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1].signif(3)}" + + / show warnings %p + - if !prediction[:warning].nil? + %b Warnings: + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"#{prediction[:warning]}"}} - else - @dbhit[i] = false %p @@ -81,4 +88,8 @@ / always show the neighbors table, message is given there = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit + +%div.modal.fade{:id=>"details0", :role=>"dialog"} + %div.modal-dialog.modal-lg + %div.modal-content diff --git a/views/style.scss b/views/style.scss index 49e03ab..2c84781 100644 --- a/views/style.scss +++ b/views/style.scss @@ -51,10 +51,12 @@ ul.share-buttons{ padding: 0 2px 1px 2px !important; } .page-header{ - margin:20px 0 20px; - text-align:justify; + background-color: #fff; + padding:20px 0 20px 0; + margin: 0; + text-align:center; display:inline-block; - width:98.5%; + width:100%; } .share{ width: 30px; @@ -62,9 +64,13 @@ ul.share-buttons{ } supporters{ background-color: white; - + text-align:center; img{ width: 200px; margin-right: 1em; } } + +.footer{ + margin-top:3em; +} diff --git a/views/validation.haml b/views/validation.haml deleted file mode 100644 index fd63ea6..0000000 --- a/views/validation.haml +++ /dev/null @@ -1,16 +0,0 @@ -- case @model_type -- when "classification" - - prediction = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numCorrect"] + @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numIncorrect"] - %p= "Number of predictions: #{prediction}" - - percent = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#percentCorrect"] - %p= "Correct predictions: #{percent.round(2)} %" -- when "regression" - - prediction = @cv.metadata["http://www.opentox.org/api/1.2#numInstances"].to_i - @cv.metadata["http://www.opentox.org/api/1.2#numUnpredicted"].to_i - %p= "Number of predictions: #{prediction}" - - rSquare = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rSquare"] - %p= "R-squared: #{rSquare.round(2)} %" - - rootMeanSquaredError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rootMeanSquaredError"] - %p= "Root Mean Square Error: #{rootMeanSquaredError.round(2)} %" - - meanAbsoluteError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#meanAbsoluteError"] - %p= "Mean Absolute Error: #{meanAbsoluteError.round(2)} %" - |