diff options
| author | gebele <gebele@in-silico.ch> | 2016-11-24 16:31:26 +0000 |
|---|---|---|
| committer | gebele <gebele@in-silico.ch> | 2016-11-24 16:31:26 +0000 |
| commit | bfd31ed2c9d0cde8a53238c7368eb3d49c580b7d (patch) | |
| tree | 91c3a2865302e1017db0dffb6015dfa3eb6c476f | |
| parent | f0588c7e072ea3e22f26916d669e9baaa8fa3197 (diff) | |
| parent | f86c084311282036ffa7b4588c0fa0d5b59af95b (diff) | |
fixed merge
35 files changed, 1112 insertions, 172 deletions
@@ -0,0 +1,29 @@ +Frequently Asked Questions +========================== +<br> +####How does this prediction works? +> + +####You talk about significant fragments. Where can I find them? +> We will show up those significant fragments in a further version. + +####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. + +####What is three times independent validation about? +> + +####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). @@ -1,6 +1,9 @@ source "https://rubygems.org" gemspec +gem "lazar", :path => "../lazar" +gem "gem-path" gem "sinatra" +gem "sinatra-reloader" gem "haml" gem "sass" -gem "lazar", :path => "../lazar" +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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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 @@ -1,10 +0,0 @@ -IST Software&Services GUI - -installation: -- bundle install -- ~/.opentox/config/lazar-gui.rb (point to services) - -usage: --start services --run 'unicorn -D' --visit 'localhost:8080' diff --git a/README.md b/README.md new file mode 100644 index 0000000..2142dd5 --- /dev/null +++ b/README.md @@ -0,0 +1,15 @@ +IST Software&Services GUI +========================= + +Installation: +------------- + bundle install + +Usage: +------ + sudo /etc/init.d/mongod start + unicorn -D + +Visit: +------ + http://localhost:8080 @@ -1 +1 @@ -0.1.0 +1.1.0 diff --git a/application.rb b/application.rb index fc7e415..5f64b84 100644 --- a/application.rb +++ b/application.rb @@ -1,4 +1,5 @@ -require_relative 'helper.rb' +#require_relative 'helper.rb' +require 'rdiscount' include OpenTox #require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb") # until added to ot-tools @@ -19,19 +20,36 @@ helpers do end +before do + @version = File.read("VERSION").chomp +end + get '/?' do redirect to('/predict') end get '/predict/?' do @models = OpenTox::Model::Prediction.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] - return haml :model_details, :layout=> false, :locals => {:model => model} + crossvalidations = OpenTox::Validation::RepeatedCrossValidation.find(model.repeated_crossvalidation_id).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 + + return haml :model_details, :layout=> false, :locals => {:model => model, :crossvalidations => crossvalidations} end get '/jme_help/?' do @@ -292,6 +310,17 @@ post '/predict/?' do end end +get '/license' do + @license = RDiscount.new(File.read("LICENSE.md")).to_html + haml :license, :layout => false +end + +=begin +get '/faq' do + @faq = RDiscount.new(File.read("FAQ.md")).to_html + haml :faq, :layout => :faq_layout +end +=end get '/style.css' do headers 'Content-Type' => 'text/css; charset=utf-8' scss :style diff --git a/bin/lazar-start b/bin/lazar-start new file mode 100755 index 0000000..73f6d91 --- /dev/null +++ b/bin/lazar-start @@ -0,0 +1,8 @@ +#!/usr/bin/env ruby +bin_dir = File.expand_path(File.dirname(__FILE__)) +shell_script_path = File.join(bin_dir, 'lazar-start.sh') +app_dir = File.expand_path('..') +unicorn_conf = File.join(app_dir, 'unicorn.rb') + +`#{shell_script_path}` +`#{unicorn_conf}` diff --git a/bin/lazar-start.sh b/bin/lazar-start.sh new file mode 100755 index 0000000..9072150 --- /dev/null +++ b/bin/lazar-start.sh @@ -0,0 +1,8 @@ +#!/bin/bash +sudo mongod & +R CMD Rserve +LAZARPATH=$(gem path lazar-gui) +cd $LAZARPATH +unicorn -c unicorn.rb -E production -D + +exit 0 diff --git a/bin/lazar-stop b/bin/lazar-stop new file mode 100755 index 0000000..67e72e9 --- /dev/null +++ b/bin/lazar-stop @@ -0,0 +1,6 @@ +#!/usr/bin/env ruby +bin_dir = File.expand_path(File.dirname(__FILE__)) +shell_script_path = File.join(bin_dir, 'lazar-stop.sh') + +`#{shell_script_path}` + diff --git a/bin/lazar-stop.sh b/bin/lazar-stop.sh new file mode 100755 index 0000000..eea6815 --- /dev/null +++ b/bin/lazar-stop.sh @@ -0,0 +1,52 @@ +#!/bin/bash +grep_lazar=`ps aux | grep -v grep | grep lazar-start` +grep_mongo=`ps aux | grep -v grep | grep mongod` +grep_rserve=`ps aux | grep -v grep | grep Rserve` +grep_unicorn=`ps aux | grep -v grep | grep unicorn` + +# lazar +if [ ${#grep_lazar} -gt 0 ] +then + PID=`ps ax | grep -v grep | grep lazar-start | awk '{ print $1 }'` + for i in "${PID}" + do + `kill $i` + done +else + echo "Lazar is stopped." +fi + +# mongod +if [ ${#grep_mongo} -gt 0 ] +then + PID=`ps ax | grep -v grep | grep mongod | awk '{ print $1 }'` + for i in "${PID}" + do + `sudo kill $i` + done +else + echo "MongoDB is not running." +fi + +# rserve +if [ ${#grep_rserve} -gt 0 ] +then + PID=`ps ax | grep -v grep | grep Rserve | awk '{ print $1 }'` + for i in "${PID}" + do + `kill $i` + done +else + echo "Rserve is not running." +fi + +# unicorn +if [ ${#grep_unicorn} -gt 0 ] +then + PID=`ps ax | grep -v grep | grep unicorn | awk '{ print $1 }'` + `kill ${PID[0]}` +else + echo "Unicorn is not running." +fi + +exit 0 @@ -1,5 +1,6 @@ -SERVICE = "lazar" +ENV["LAZAR_ENV"] = "development" require 'bundler' Bundler.require require File.expand_path './application.rb' +require "sinatra/reloader" if development? run Sinatra::Application diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index dd852a0..af5f0f9 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -8,17 +8,22 @@ Gem::Specification.new do |s| s.homepage = "http://github.com/opentox/lazar-gui" s.summary = %q{lazar-gui} s.description = %q{Graphical User Interface for Lazar Toxicology Predictions} - s.license = 'GPL-3' - + s.license = 'GPL-3.0' + s.executables = ["lazar-start", "lazar-stop"] s.rubyforge_project = "lazar-gui" - s.files = `git ls-files`.split("\n") - s.required_ruby_version = '>= 1.9.2' - #s.add_runtime_dependency "opentox-server" - s.add_runtime_dependency "lazar" - s.add_runtime_dependency "sinatra" - s.add_runtime_dependency "haml" - s.add_runtime_dependency "sass" - s.add_runtime_dependency "unicorn" + 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.post_install_message = %q{ + Service cmds: + lazar-start & + lazar-stop + } end diff --git a/public/images/Email.png b/public/images/Email.png Binary files differnew file mode 100755 index 0000000..1e5c8bf --- /dev/null +++ b/public/images/Email.png diff --git a/public/images/Facebook.png b/public/images/Facebook.png Binary files differnew file mode 100755 index 0000000..3d249fd --- /dev/null +++ b/public/images/Facebook.png diff --git a/public/images/Google+.png b/public/images/Google+.png Binary files differnew file mode 100644 index 0000000..9db76fd --- /dev/null +++ b/public/images/Google+.png diff --git a/public/images/IST_logo_s.png b/public/images/IST_logo_s.png Binary files differnew file mode 100644 index 0000000..eff71af --- /dev/null +++ b/public/images/IST_logo_s.png diff --git a/public/images/LinkedIn.png b/public/images/LinkedIn.png Binary files differnew file mode 100644 index 0000000..dcdda37 --- /dev/null +++ b/public/images/LinkedIn.png diff --git a/public/images/Twitter.png b/public/images/Twitter.png Binary files differnew file mode 100644 index 0000000..05e0c2c --- /dev/null +++ b/public/images/Twitter.png diff --git a/public/images/bfr_logo.gif b/public/images/bfr_logo.gif Binary files differnew file mode 100644 index 0000000..1d6d36b --- /dev/null +++ b/public/images/bfr_logo.gif diff --git a/public/images/enm_logo.png b/public/images/enm_logo.png Binary files differnew file mode 100644 index 0000000..cac2dd3 --- /dev/null +++ b/public/images/enm_logo.png diff --git a/public/images/nestec.jpg b/public/images/nestec.jpg Binary files differnew file mode 100644 index 0000000..ba1c335 --- /dev/null +++ b/public/images/nestec.jpg diff --git a/public/images/ot_logo.png b/public/images/ot_logo.png Binary files differnew file mode 100644 index 0000000..7dfa6f9 --- /dev/null +++ b/public/images/ot_logo.png @@ -1,2 +1,7 @@ #worker_processes 4 timeout 6000 +listen 8088 +log_dir = "#{ENV['HOME']}" +log_file = File.join log_dir, "lazar.log" +stderr_path log_file +stdout_path log_file diff --git a/views/details.haml b/views/details.haml index 8a57440..bb8250d 100644 --- a/views/details.haml +++ b/views/details.haml @@ -19,6 +19,6 @@ %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.haml b/views/faq.haml new file mode 100644 index 0000000..818b96a --- /dev/null +++ b/views/faq.haml @@ -0,0 +1,2 @@ +%div.well.faq + = @faq diff --git a/views/faq_layout.haml b/views/faq_layout.haml new file mode 100644 index 0000000..a9b6664 --- /dev/null +++ b/views/faq_layout.haml @@ -0,0 +1,67 @@ +!!! +%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 60f2bb3..dddf854 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -4,7 +4,7 @@ %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 Toxicity Predictions + %title lazar Toxicity Predictions %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'}"} @@ -15,8 +15,8 @@ %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"} - %body{:style=>"background-color:#E7E7E7"} + %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. @@ -24,11 +24,38 @@ %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;"} + %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 1em;"} Lazar Toxicity Predictions - + %h1.media-heading + lazar toxicity predictions + %div.col-md-2 + %h1.media-heading + %small + %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar + %div.container-fluid + %topline + %div.row + %div.col-md-8 + 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"} + %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"} + %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+"} + %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"} + %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"} + %img.share{:src=>"/images/Facebook.png"} + %div.row + Previous version: + %a{:href=>"http://lazar-old.in-silico.ch", :rel => "external"} lazar-old :javascript $(document).ready(function(){ $("#back-top").hide(); @@ -36,14 +63,35 @@ $(this).attr('src', '/images/blind.png'); }); }); + $(document).ready(function(){ + $('[data-toggle="popover"]').popover(); + $('.modal').on('hidden.bs.modal', function () { + $(this).removeData('bs.modal'); + }); + }); = 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} + %div.row + %div.col-md-12 + %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 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/", :rel=>"external"} + %img{:src=>"/images/ot_logo.png"} + %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", :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 e5886e7..7646471 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -1,28 +1,39 @@ %b Model: %br Source: -%a{:href=>model.source, :target=>"external"} +%a{:href=>model.source, :rel=>"external"} = model.source %br -= "Algorithm:\tLAZAR" -%br - model.classification? ? type = "Classification" : type = "Regression" = "Type:\t" = type %br -- training_dataset = OpenTox::Dataset.find model.training_dataset.id -= "Training dataset:\t" -= training_dataset.source.split("/").last -%br +- training_dataset = OpenTox::Dataset.find model.model.training_dataset_id = "Training compounds:\t" = training_dataset.compounds.size - +%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 -%b Crossvalidation (3 independent): +- 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 @@ -36,93 +47,89 @@ Source: = "Accuracy:\t" = cv.accuracy.round(3) if cv.accuracy %br - = "Weighted Accuracy:\t" + = "Weighted accuracy:\t" = cv.weighted_accuracy.round(3) if cv.weighted_accuracy %br = "True positive rate:\t" - = cv.true_rate["active"].round(3) if cv.true_rate["active"] + = cv.true_rate["active"].round(3) if cv.true_rate %br = "True negative rate:\t" - = cv.true_rate["inactive"].round(3) if cv.true_rate["inactive"] + = cv.true_rate["inactive"].round(3) if cv.true_rate %br = "Positive predictive value:\t" - = cv.predictivity["active"].round(3) if cv.predictivity["active"] + = cv.predictivity["active"].round(3) if cv.predictivity %br = "Negative predictive value:\t" - = cv.predictivity["inactive"].round(3) if cv.predictivity["inactive"] + = cv.predictivity["inactive"].round(3) if cv.predictivity %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 - -#%p - = "Confidence plot:" - -#%p{:id=>"confp#{cv.id}", :style=>"transform:scale(0.5);margin-left:-30%;margin-top:-30%;padding:0;"} - = cv.confidence_plot + /= "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 - = "Weighted root mean squared error:\t" - = cv.weighted_rmse.round(3) if cv.weighted_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 - = "Weighted mean absolute error:\t" - = cv.weighted_mae.round(3) if cv.weighted_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 - -#%p - = "Correlation plot" - -#%p{:id=>"corrp#{cv.id}", :style=>"transform:scale(0.5);margin-left:-30%;margin-top:-30%;margin-bottom:0;padding:0;"} - =cv.correlation_plot - -#%p - = "Confidence plot:" - -#%p{:id=>"confp#{cv.id}", :style=>"transform:scale(0.5);margin-left:-30%;margin-top:-30%;margin-bottom:0;padding:0;"} - = cv.confidence_plot + %br + /= "Confidence plot:" + /%p.plot + / %img{:src=>"/confp#{cv.id}.svg"} + /%br + /= "Correlation plot" + /%p.plot + / %img{:src=>"/corrp#{cv.id}.svg"} + %br diff --git a/views/neighbors.haml b/views/neighbors.haml index 6001605..d9f2796 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -9,7 +9,17 @@ #tabs %ul.nav.nav-tabs.nav-justified{:id=>"neighborTabs", :role=>"tablist"} / each model a tab head ; + / hash for predictionFeature + - predictionFeature = {} - @models.each_with_index do |model,i| + / get predictionFeature type + - m = Model::Lazar.find model.model_id.to_s + - predFeature = Feature.find m.prediction_feature_id.to_s + / define feature type (numeric : nominal) + - predFeatureType = (predFeature.numeric? ? "numeric" : "nominal") + / use prediction feature id for neighbor compound features + - predFeatureId = m.prediction_feature_id.to_s + - predictionFeature[i] = {"id" => predFeatureId, "type" => predFeatureType} %li{:class => ("active" if i == 0)} %a{:href => "#results_#{i+1}", :id => "linkTab#{i+1}", data: {toggle:"tab"}} = "#{model.endpoint} (#{model.species})" @@ -28,8 +38,8 @@ $("table##{j+1}").tablesorter({ debug: false, theme: "bootstrap", - headerTemplate: '{content} {icon}', - widgets: ['zebra', 'columns', 'uitheme', 'stickyHeaders'], + headerTemplate: '', + widgets: ['columns', 'uitheme', 'stickyHeaders'], widgetOptions: { stickyHeaders_attachTo : '.tab-content', stickyHeaders : '', @@ -43,50 +53,45 @@ stickyHeaders_yScroll : null, stickyHeaders_filteredToTop: true }, - headers: {0: {sorter: false}, 3: {sorter: false}}, sortList: [[2,1]], + headers: {sorter: false}, widthFixed: false }); }); - if prediction[:neighbors].size > 0 %div.table-responsive - %table.tablesorter{:id=>"#{j+1}", :style=>"border-style: solid;"} + %table{:id=>"#{j+1}", :style=>"border-style: solid;"} %thead %tr - %th{:style =>"vertical-align:middle;"} + %th.sorter-false{:style =>"vertical-align:middle;"} Compound - %th{:style =>"vertical-align:middle;"} + %th.sorter-false{:style =>"vertical-align:middle;"} Measured Activity - %th{:style =>"vertical-align:middle;"} + %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;"} + %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;"} / %th{:style =>"vertical-align:middle;"} / Supporting Information - %span - %tr - %td - %td{:style=>"font-size:x-small;padding:0px;"} - / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", data: {toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"} - %td{:style=>"font-size:x-small;padding:0px;"} - / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", data: {toggle:"popover", placement:"auto", html:"true", content:"LAZAR calculates activity specific similarities based on the presence of statistically significant fragments. This procedure will <ul><li>consider only those parts of a chemical structure that are relevant for a particular endpoint</li><li>ignore inert parts of the structure</li><li>lead to different similarities, depending on the toxic endpoint Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.</li></ul>"}, :style=>"z-index:auto+10;"} - / %td %tbody - type = @model_types[j] + - unit = @models[j].unit - prediction[:neighbors].uniq.each_with_index do |neighbor,count| %tr / Compound + - 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[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}} - %p= Compound.find(neighbor[0]).svg - %p= Compound.find(neighbor[0]).smiles - - c = Compound.find(neighbor[0]) - //- mw = c.molecular_weight + /%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 + %p= c.smiles / Measured Activity %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"} - = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : neighbor[2].join(", ") - / Similarity + = (type == "Regression" ? "#{neighbor[:measurement].delog10}" + " (#{unit})" : neighbor[:measurement]) + %br + = "#{c.mmol_to_mg(neighbor[:measurement].delog10)}" + " (#{(unit =~ /\b(mol\/L)\b/) ? "mg/L" : "mg/kg_bw/day"})" if type == "Regression" + / 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[1] != nil ? neighbor[1].round(2) : "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 7f19071..66006d4 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -162,6 +162,7 @@ document.getElementById("details#{model.id}").appendChild(details); $(button).show(); $(image).hide(); + addExternalLinks(); }); } } diff --git a/views/prediction.haml b/views/prediction.haml index 8d7e3d0..2454aca 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -12,7 +12,7 @@ / displays all prediction result in first table %h3 Prediction Results: %div.table-responsive - %table.table.table-bordered{:id=>"overview", :style=>"background-color:white;"} + %table.table.table-bordered{:id=>"overview"} %tbody %tr %td{:id=>"compound", :style=>"vertical-align:top;"} @@ -24,21 +24,25 @@ - @predictions.each_with_index do |prediction,i| - type = @models[i].model.class.to_s.match("Classification") ? "Classification" : "Regression" - @model_types[i] = type + - unit = @models[i].unit %td{:style=>"vertical-align:top;white-space:nowrap;"} %b{:class => "title"} = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})" %p - - if prediction[:confidence] == "measured" + - if prediction[:warning] =~ /\b(identical)\b/i - @dbhit[i] = true %p + /TODO combine with regular view, if prediction value is present %b Measured activity: - - p prediction[:value] + - 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 + " (#{@models[i].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ") + = (type == "Regression") ? prediction[:value].collect{|value| "#{value} (#{unit}) , #{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ") - else - = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value] - %p + = (type == "Regression") ? "#{prediction[:value]} (#{unit}), #{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] + %p %b Compound is part of the training dataset + / warning popover + %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"#{prediction[:warning]}"}} - elsif prediction[:neighbors].size > 0 %p / model type (classification|regression) @@ -46,22 +50,38 @@ = type %br %b Prediction: - = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value] - / TODO update description - / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}} + / 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 + = (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] + / 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. %br - / TODO probability - %b Confidence: - = prediction[:confidence].round(2) - / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {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."}} + - if type == "Regression" + %b 95% Prediction interval: + - interval = (prediction[:prediction_interval].nil? ? ["- -","- -"] : prediction[:prediction_interval]) + / 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."}} + %br + = "#{interval[0].delog10} - #{interval[1].delog10} (#{unit})" + %br + = "#{@compound.mmol_to_mg(interval[0].delog10)} - #{@compound.mmol_to_mg(interval[1].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 + = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}" + / probability 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."}} %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", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} 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", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} 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 %p - else diff --git a/views/style.scss b/views/style.scss index 9a3c9df..2c84781 100644 --- a/views/style.scss +++ b/views/style.scss @@ -1,3 +1,6 @@ +body { + background-color:#E7E7E7; +} table.table-borderless tbody tr td{ border-top: none; } @@ -16,3 +19,58 @@ h4.head-back, h5.head-back{ height: 5em; } } +img { + max-width: 100%; + max-height: 100%; +} + +.plot { + height: 300px; + width: 300px; +} +.faq { + text-align: block; + margin-left:15%; + margin-right:15%; + margin-top:2%; +} +.faq h1 { + text-align: center; +} +.tablesorter-bootstrap thead .sorter-false { + cursor: default; +} +ul.share-buttons{ + list-style: none; +} +.dropdown-menu { + min-width: 0px !important; + width:60px; +} +.dropdown-menu a { + padding: 0 2px 1px 2px !important; +} +.page-header{ + background-color: #fff; + padding:20px 0 20px 0; + margin: 0; + text-align:center; + display:inline-block; + width:100%; +} +.share{ + width: 30px; + padding-right: 5px; +} +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)} %" - |
