From ddbe5c5478c7dd71d9c851008340e28a61d5ba33 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 27 Oct 2015 12:24:58 +0000 Subject: enabled batch --- views/predict.haml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/views/predict.haml b/views/predict.haml index 9863cd9..0dc767b 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -125,12 +125,11 @@ %br %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'} %p - // disable for public version %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"} + %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv"} %fieldset#middle.well %h2 2. Select one or more endpoints -- cgit v1.2.3 From 41f948d58ba99a635ae7e04573bd368d9ab34d99 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 27 Oct 2015 12:26:14 +0000 Subject: enabled batch --- views/predict.haml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/views/predict.haml b/views/predict.haml index 0dc767b..a4fa080 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -126,7 +126,7 @@ %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'} %p %label{:for=>"fileselect"} - or upload a CSV file for batch predictions (disabled in public version) + or upload a CSV file for batch predictions %br %span.btn.btn-default.btn-file %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv"} -- cgit v1.2.3 From d2d8db1e59e830b1a24e9b8d270a3b393d746b6c Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 28 Oct 2015 13:58:45 +0000 Subject: consisten use of brackets for units; collect measured activity for equal neighbors --- views/batch.haml | 3 +-- views/neighbors.haml | 4 ++-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/views/batch.haml b/views/batch.haml index 8389651..ec987c4 100644 --- a/views/batch.haml +++ b/views/batch.haml @@ -44,7 +44,7 @@ %br %b Prediction: / TODO scientific notation - = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit}" : prediction[:value] + = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value] %br / TODO probability %b Confidence: @@ -53,4 +53,3 @@ - else %p = "Not enough similar compounds
in training dataset." - %p diff --git a/views/neighbors.haml b/views/neighbors.haml index 21b4b35..a741b45 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -58,7 +58,7 @@ / %td %tbody - type = @model_types[j] - - prediction[:neighbors].each_with_index do |neighbor,count| + - prediction[:neighbors].uniq.each_with_index do |neighbor,count| %tr / Compound %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"} @@ -67,7 +67,7 @@ %p= Compound.find(neighbor[0]).smiles / Measured Activity %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"} - = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join(", ") : neighbor[2].join(", ") + = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("
") : neighbor[2].join(", ") / Similarity %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? -- cgit v1.2.3 From b452a81e9c0a470bf9aa51f0192378f5fba5177a Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 29 Oct 2015 09:54:15 +0000 Subject: trim and log SMILES input --- application.rb | 14 ++++++++------ views/predict.haml | 2 +- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/application.rb b/application.rb index 9c9cabb..d77842d 100644 --- a/application.rb +++ b/application.rb @@ -259,12 +259,14 @@ post '/predict/?' do # validate identifier input # transfered input if !params[:identifier].blank? - @identifier = params[:identifier] - begin - # get compound from SMILES - @compound = Compound.from_smiles @identifier - rescue - @error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string." + # remove whitespaces they terminate a SMILES string + # can result in wrong conversion for compound object + @identifier = params[:identifier].gsub(/\s+/, "") + $logger.debug "input:#{@identifier}" + # get compound from SMILES + @compound = Compound.from_smiles @identifier + if @compound.blank? + @error_report = "Attention, '#{@identifier}' is not a valid SMILES string." return haml :error end diff --git a/views/predict.haml b/views/predict.haml index a4fa080..7f19071 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -24,7 +24,7 @@ }); function getInput(){ - identifier = document.getElementById("identifier").value; + identifier = document.getElementById("identifier").value.trim(); fileselect = document.getElementById("fileselect").value; if (fileselect != ""){ return 1; -- cgit v1.2.3 From 95236e48e8a1da009e6b5ab1789f0de37dde36f5 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 29 Oct 2015 12:55:57 +0000 Subject: patch merge --- application.rb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/application.rb b/application.rb index d77842d..229f3a1 100644 --- a/application.rb +++ b/application.rb @@ -259,9 +259,7 @@ post '/predict/?' do # validate identifier input # transfered input if !params[:identifier].blank? - # remove whitespaces they terminate a SMILES string - # can result in wrong conversion for compound object - @identifier = params[:identifier].gsub(/\s+/, "") + @identifier = params[:identifier] $logger.debug "input:#{@identifier}" # get compound from SMILES @compound = Compound.from_smiles @identifier -- cgit v1.2.3 From efd241beab11fbfc200f0c32ffb9e198ed406c83 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 29 Oct 2015 18:20:39 +0000 Subject: added mg/kg_bw/day --- application.rb | 6 ++++-- views/batch.haml | 5 +++-- views/neighbors.haml | 6 ++++-- views/prediction.haml | 6 +++--- 4 files changed, 14 insertions(+), 9 deletions(-) diff --git a/application.rb b/application.rb index 229f3a1..1763e3a 100644 --- a/application.rb +++ b/application.rb @@ -202,14 +202,16 @@ get '/predict/?:csv?' do model = array[0] prediction = array[1] compound = key.smiles + mw = key.molecular_weight + weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw) endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" if prediction[:confidence] == "measured" type = "" - pred = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value] + pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value] confidence = "measured activity" elsif prediction[:neighbors].size > 0 type = model.model.class.to_s.match("Classification") ? "Classification" : "Regression" - pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit}" : prediction[:value] + pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit} | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value] confidence = prediction[:confidence] else type = "" diff --git a/views/batch.haml b/views/batch.haml index ec987c4..f593188 100644 --- a/views/batch.haml +++ b/views/batch.haml @@ -18,6 +18,7 @@ / key = compound, values = array of arrays with model, prediction - @batch.each do |key, values| - compound = key + - mw = compound.molecular_weight %tr %td{:style=>"vertical-align:top;"} %p= compound.svg @@ -34,7 +35,7 @@ %p / TODO fix scientific notation from database %b Measured activity: - = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value] + = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] %p Compound is part of the training dataset - elsif prediction[:neighbors].size > 0 %p @@ -44,7 +45,7 @@ %br %b Prediction: / TODO scientific notation - = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value] + = 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: diff --git a/views/neighbors.haml b/views/neighbors.haml index a741b45..4a1f3ea 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -65,9 +65,11 @@ /%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 / Measured Activity - %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"} - = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("
") : neighbor[2].join(", ") + %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, mw); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("
") : neighbor[2].join(", ") / Similarity %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? diff --git a/views/prediction.haml b/views/prediction.haml index ef0c5db..11d542e 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -18,6 +18,7 @@ %td{:id=>"compound", :style=>"vertical-align:top;"} %p= @compound.svg %p= @compound.smiles + - mw = @compound.molecular_weight - @model_types = {} - @dbhit = {} - @predictions.each_with_index do |prediction,i| @@ -32,7 +33,7 @@ %p / TODO fix scientific notation from database %b Measured activity: - = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit})" : prediction[:value] + = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] %p Compound is part of the training dataset - elsif prediction[:neighbors].size > 0 %p @@ -41,8 +42,7 @@ = type %br %b Prediction: - / TODO scientific notation - = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit})" : prediction[:value] + = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (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 Please keep in mind that predictions are based on the measured activities of neighbors."}} %br -- cgit v1.2.3 From a348f222c0b32bbb308083bb03127fe55b1563dc Mon Sep 17 00:00:00 2001 From: gebele Date: Fri, 30 Oct 2015 08:26:04 +0000 Subject: fixed weight for multiple database hits in prediction --- application.rb | 23 +++++++++++++++++------ views/batch.haml | 12 +++++++----- views/prediction.haml | 10 +++++++--- 3 files changed, 31 insertions(+), 14 deletions(-) diff --git a/application.rb b/application.rb index 1763e3a..fc7e415 100644 --- a/application.rb +++ b/application.rb @@ -203,22 +203,33 @@ get '/predict/?:csv?' do prediction = array[1] compound = key.smiles mw = key.molecular_weight - weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw) endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" if prediction[:confidence] == "measured" - type = "" - pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value] - confidence = "measured activity" + 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" + 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] + 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] + pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value] confidence = prediction[:confidence] else type = "" pred = "Not enough similar compounds in training dataset." confidence = "" end - @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n" + @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n" unless prediction[:value].is_a?(Array) end end @csv diff --git a/views/batch.haml b/views/batch.haml index f593188..9bfa67e 100644 --- a/views/batch.haml +++ b/views/batch.haml @@ -33,10 +33,13 @@ %p - if prediction[:confidence] == "measured" %p - / TODO fix scientific notation from database - %b Measured activity: - = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] - %p Compound is part of the training dataset + %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("
") : 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] + %p + %b Compound is part of the training dataset - elsif prediction[:neighbors].size > 0 %p / model type (classification|regression) @@ -44,7 +47,6 @@ = model.model.class.to_s.match("Classification") ? "Classification" : "Regression" %br %b Prediction: - / TODO scientific notation = 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 diff --git a/views/prediction.haml b/views/prediction.haml index 11d542e..a74b95a 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -31,10 +31,14 @@ - if prediction[:confidence] == "measured" - @dbhit[i] = true %p - / TODO fix scientific notation from database %b Measured activity: - = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] - %p Compound is part of the training dataset + - 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, mw); '%.2e' % v + " (#{@models[i].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("
") : prediction[:value].join(", ") + - else + = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (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) -- cgit v1.2.3 From f7680842ee830af78d860b3a0a09b654368df90a Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 14 Jan 2016 09:37:39 +0000 Subject: changed weight method for lazar v8-nestec release --- views/neighbors.haml | 4 ++-- views/prediction.haml | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/views/neighbors.haml b/views/neighbors.haml index 4a1f3ea..a69f38b 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -66,10 +66,10 @@ %p= Compound.find(neighbor[0]).svg %p= Compound.find(neighbor[0]).smiles - c = Compound.find(neighbor[0]) - - mw = c.molecular_weight + //- mw = c.molecular_weight / 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, mw); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("
") : neighbor[2].join(", ") + = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("
") : neighbor[2].join(", ") / Similarity %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? diff --git a/views/prediction.haml b/views/prediction.haml index a74b95a..8d7e3d0 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -18,7 +18,7 @@ %td{:id=>"compound", :style=>"vertical-align:top;"} %p= @compound.svg %p= @compound.smiles - - mw = @compound.molecular_weight + -#- mw = @compound.molecular_weight - @model_types = {} - @dbhit = {} - @predictions.each_with_index do |prediction,i| @@ -34,9 +34,9 @@ %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, mw); '%.2e' % v + " (#{@models[i].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("
") : prediction[:value].join(", ") + = (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("
") : prediction[:value].join(", ") - else - = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] + = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value] %p %b Compound is part of the training dataset - elsif prediction[:neighbors].size > 0 @@ -46,7 +46,7 @@ = type %br %b Prediction: - = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] + = (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 Please keep in mind that predictions are based on the measured activities of neighbors."}} %br -- cgit v1.2.3 From f0588c7e072ea3e22f26916d669e9baaa8fa3197 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 26 Jan 2016 11:45:30 +0000 Subject: enabled sticky headers for neighbors table --- views/neighbors.haml | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/views/neighbors.haml b/views/neighbors.haml index a69f38b..6001605 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -29,7 +29,20 @@ debug: false, theme: "bootstrap", headerTemplate: '{content} {icon}', - widgets: ['zebra', 'columns', 'uitheme'], + widgets: ['zebra', 'columns', 'uitheme', 'stickyHeaders'], + widgetOptions: { + stickyHeaders_attachTo : '.tab-content', + stickyHeaders : '', + stickyHeaders_offset : 0, + stickyHeaders_cloneId : '-sticky', + stickyHeaders_addResizeEvent : true, + stickyHeaders_includeCaption : true, + stickyHeaders_zIndex : 2, + stickyHeaders_attachTo : null, + stickyHeaders_xScroll : null, + stickyHeaders_yScroll : null, + stickyHeaders_filteredToTop: true + }, headers: {0: {sorter: false}, 3: {sorter: false}}, sortList: [[2,1]], widthFixed: false -- cgit v1.2.3 From f86c084311282036ffa7b4588c0fa0d5b59af95b Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 24 Nov 2016 16:03:09 +0000 Subject: several fixes; works with lazar tree e111369ce5564f159b3f5f85c92afdd22352eaa1 --- Gemfile | 4 +- LICENSE.md | 596 +++++++++++++++++++++++++++++++++++++++++++++++ VERSION | 2 +- application.rb | 18 +- config.ru | 3 +- views/details.haml | 2 +- views/layout.haml | 18 +- views/license.haml | 1 + views/model_details.haml | 134 ++++++----- views/neighbors.haml | 13 +- views/predict.haml | 1 + views/prediction.haml | 35 +-- views/style.scss | 14 +- views/validation.haml | 16 -- 14 files changed, 743 insertions(+), 114 deletions(-) create mode 100644 LICENSE.md create mode 100644 views/license.haml delete mode 100644 views/validation.haml diff --git a/Gemfile b/Gemfile index 7bade23..c86c89a 100644 --- a/Gemfile +++ b/Gemfile @@ -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. <> + +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. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change all versions of a +program--to make sure it remains free software for all its users. We, the Free +Software Foundation, use the GNU General Public License for most of our software; it +applies also to any other work released this way by its authors. You can apply it to +your programs, too. + +When we speak of free software, we are referring to freedom, not price. Our General +Public Licenses are designed to make sure that you have the freedom to distribute +copies of free software (and charge for them if you wish), that you receive source +code or can get it if you want it, that you can change the software or use pieces of +it in new free programs, and that you know you can do these things. + +To protect your rights, we need to prevent others from denying you these rights or +asking you to surrender the rights. Therefore, you have certain responsibilities if +you distribute copies of the software, or if you modify it: responsibilities to +respect the freedom of others. + +For example, if you distribute copies of such a program, whether gratis or for a fee, +you must pass on to the recipients the same freedoms that you received. You must make +sure that they, too, receive or can get the source code. And you must show them these +terms so they know their rights. + +Developers that use the GNU GPL protect your rights with two steps: (1) assert +copyright on the software, and (2) offer you this License giving you legal permission +to copy, distribute and/or modify it. + +For the developers' and authors' protection, the GPL clearly explains that there is +no warranty for this free software. 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Source Code. + +The “source code” for a work means the preferred form of the work for +making modifications to it. “Object code” means any non-source form of a +work. + +A “Standard Interface” means an interface that either is an official +standard defined by a recognized standards body, or, in the case of interfaces +specified for a particular programming language, one that is widely used among +developers working in that language. + +The “System Libraries” of an executable work include anything, other than +the work as a whole, that (a) is included in the normal form of packaging a Major +Component, but which is not part of that Major Component, and (b) serves only to +enable use of the work with that Major Component, or to implement a Standard +Interface for which an implementation is available to the public in source code form. +A “Major Component”, in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system (if any) on which +the executable work runs, or a compiler used to produce the work, or an object code +interpreter used to run it. + +The “Corresponding Source” for a work in object code form means all the +source code needed to generate, install, and (for an executable work) run the object +code and to modify the work, including scripts to control those activities. 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This License +explicitly affirms your unlimited permission to run the unmodified Program. The +output from running a covered work is covered by this License only if the output, +given its content, constitutes a covered work. This License acknowledges your rights +of fair use or other equivalent, as provided by copyright law. + +You may make, run and propagate covered works that you do not convey, without +conditions so long as your license otherwise remains in force. You may convey covered +works to others for the sole purpose of having them make modifications exclusively +for you, or provide you with facilities for running those works, provided that you +comply with the terms of this License in conveying all material for which you do not +control copyright. 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Protecting Users' Legal Rights From Anti-Circumvention Law. + +No covered work shall be deemed part of an effective technological measure under any +applicable law fulfilling obligations under article 11 of the WIPO copyright treaty +adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention +of such measures. + +When you convey a covered work, you waive any legal power to forbid circumvention of +technological measures to the extent such circumvention is effected by exercising +rights under this License with respect to the covered work, and you disclaim any +intention to limit operation or modification of the work as a means of enforcing, +against the work's users, your or third parties' legal rights to forbid circumvention +of technological measures. + +### 4. Conveying Verbatim Copies. + +You may convey verbatim copies of the Program's source code as you receive it, in any +medium, provided that you conspicuously and appropriately publish on each copy an +appropriate copyright notice; keep intact all notices stating that this License and +any non-permissive terms added in accord with section 7 apply to the code; keep +intact all notices of the absence of any warranty; and give all recipients a copy of +this License along with the Program. + +You may charge any price or no price for each copy that you convey, and you may offer +support or warranty protection for a fee. + +### 5. Conveying Modified Source Versions. + +You may convey a work based on the Program, or the modifications to produce it from +the Program, in the form of source code under the terms of section 4, provided that +you also meet all of these conditions: + +* **a)** The work must carry prominent notices stating that you modified it, and giving a +relevant date. +* **b)** The work must carry prominent notices stating that it is released under this +License and any conditions added under section 7. This requirement modifies the +requirement in section 4 to “keep intact all notices”. +* **c)** You must license the entire work, as a whole, under this License to anyone who +comes into possession of a copy. This License will therefore apply, along with any +applicable section 7 additional terms, to the whole of the work, and all its parts, +regardless of how they are packaged. 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Conveying Non-Source Forms. + +You may convey a covered work in object code form under the terms of sections 4 and +5, provided that you also convey the machine-readable Corresponding Source under the +terms of this License, in one of these ways: + +* **a)** Convey the object code in, or embodied in, a physical product (including a +physical distribution medium), accompanied by the Corresponding Source fixed on a +durable physical medium customarily used for software interchange. +* **b)** Convey the object code in, or embodied in, a physical product (including a +physical distribution medium), accompanied by a written offer, valid for at least +three years and valid for as long as you offer spare parts or customer support for +that product model, to give anyone who possesses the object code either (1) a copy of +the Corresponding Source for all the software in the product that is covered by this +License, on a durable physical medium customarily used for software interchange, for +a price no more than your reasonable cost of physically performing this conveying of +source, or (2) access to copy the Corresponding Source from a network server at no +charge. +* **c)** Convey individual copies of the object code with a copy of the written offer to +provide the Corresponding Source. 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But this requirement does not apply if +neither you nor any third party retains the ability to install modified object code +on the User Product (for example, the work has been installed in ROM). + +The requirement to provide Installation Information does not include a requirement to +continue to provide support service, warranty, or updates for a work that has been +modified or installed by the recipient, or for the User Product in which it has been +modified or installed. Access to a network may be denied when the modification itself +materially and adversely affects the operation of the network or violates the rules +and protocols for communication across the network. + +Corresponding Source conveyed, and Installation Information provided, in accord with +this section must be in a format that is publicly documented (and with an +implementation available to the public in source code form), and must require no +special password or key for unpacking, reading or copying. + +### 7. Additional Terms. + +“Additional permissions” are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. Additional +permissions that are applicable to the entire Program shall be treated as though they +were included in this License, to the extent that they are valid under applicable +law. If additional permissions apply only to part of the Program, that part may be +used separately under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option remove any +additional permissions from that copy, or from any part of it. (Additional +permissions may be written to require their own removal in certain cases when you +modify the work.) You may place additional permissions on material, added by you to a +covered work, for which you have or can give appropriate copyright permission. + +Notwithstanding any other provision of this License, for material you add to a +covered work, you may (if authorized by the copyright holders of that material) +supplement the terms of this License with terms: + +* **a)** Disclaiming warranty or limiting liability differently from the terms of +sections 15 and 16 of this License; or +* **b)** Requiring preservation of specified reasonable legal notices or author +attributions in that material or in the Appropriate Legal Notices displayed by works +containing it; or +* **c)** Prohibiting misrepresentation of the origin of that material, or requiring that +modified versions of such material be marked in reasonable ways as different from the +original version; or +* **d)** Limiting the use for publicity purposes of names of licensors or authors of the +material; or +* **e)** Declining to grant rights under trademark law for use of some trade names, +trademarks, or service marks; or +* **f)** Requiring indemnification of licensors and authors of that material by anyone +who conveys the material (or modified versions of it) with contractual assumptions of +liability to the recipient, for any liability that these contractual assumptions +directly impose on those licensors and authors. + +All other non-permissive additional terms are considered “further +restrictions” within the meaning of section 10. If the Program as you received +it, or any part of it, contains a notice stating that it is governed by this License +along with a term that is a further restriction, you may remove that term. If a +license document contains a further restriction but permits relicensing or conveying +under this License, you may add to a covered work material governed by the terms of +that license document, provided that the further restriction does not survive such +relicensing or conveying. + +If you add terms to a covered work in accord with this section, you must place, in +the relevant source files, a statement of the additional terms that apply to those +files, or a notice indicating where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the form of a +separately written license, or stated as exceptions; the above requirements apply +either way. + +### 8. Termination. + +You may not propagate or modify a covered work except as expressly provided under +this License. Any attempt otherwise to propagate or modify it is void, and will +automatically terminate your rights under this License (including any patent licenses +granted under the third paragraph of section 11). + +However, if you cease all violation of this License, then your license from a +particular copyright holder is reinstated (a) provisionally, unless and until the +copyright holder explicitly and finally terminates your license, and (b) permanently, +if the copyright holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + +Moreover, your license from a particular copyright holder is reinstated permanently +if the copyright holder notifies you of the violation by some reasonable means, this +is the first time you have received notice of violation of this License (for any +work) from that copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + +Termination of your rights under this section does not terminate the licenses of +parties who have received copies or rights from you under this License. If your +rights have been terminated and not permanently reinstated, you do not qualify to +receive new licenses for the same material under section 10. + +### 9. Acceptance Not Required for Having Copies. + +You are not required to accept this License in order to receive or run a copy of the +Program. Ancillary propagation of a covered work occurring solely as a consequence of +using peer-to-peer transmission to receive a copy likewise does not require +acceptance. However, nothing other than this License grants you permission to +propagate or modify any covered work. These actions infringe copyright if you do not +accept this License. Therefore, by modifying or propagating a covered work, you +indicate your acceptance of this License to do so. + +### 10. Automatic Licensing of Downstream Recipients. + +Each time you convey a covered work, the recipient automatically receives a license +from the original licensors, to run, modify and propagate that work, subject to this +License. You are not responsible for enforcing compliance by third parties with this +License. + +An “entity transaction” is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an organization, or +merging organizations. If propagation of a covered work results from an entity +transaction, each party to that transaction who receives a copy of the work also +receives whatever licenses to the work the party's predecessor in interest had or +could give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if the predecessor +has it or can get it with reasonable efforts. + +You may not impose any further restrictions on the exercise of the rights granted or +affirmed under this License. For example, you may not impose a license fee, royalty, +or other charge for exercise of rights granted under this License, and you may not +initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging +that any patent claim is infringed by making, using, selling, offering for sale, or +importing the Program or any portion of it. + +### 11. Patents. + +A “contributor” is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The work thus +licensed is called the contributor's “contributor version”. + +A contributor's “essential patent claims” are all patent claims owned or +controlled by the contributor, whether already acquired or hereafter acquired, that +would be infringed by some manner, permitted by this License, of making, using, or +selling its contributor version, but do not include claims that would be infringed +only as a consequence of further modification of the contributor version. For +purposes of this definition, “control” includes the right to grant patent +sublicenses in a manner consistent with the requirements of this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free patent license +under the contributor's essential patent claims, to make, use, sell, offer for sale, +import and otherwise run, modify and propagate the contents of its contributor +version. + +In the following three paragraphs, a “patent license” is any express +agreement or commitment, however denominated, not to enforce a patent (such as an +express permission to practice a patent or covenant not to sue for patent +infringement). To “grant” such a patent license to a party means to make +such an agreement or commitment not to enforce a patent against the party. + +If you convey a covered work, knowingly relying on a patent license, and the +Corresponding Source of the work is not available for anyone to copy, free of charge +and under the terms of this License, through a publicly available network server or +other readily accessible means, then you must either (1) cause the Corresponding +Source to be so available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner consistent with +the requirements of this License, to extend the patent license to downstream +recipients. “Knowingly relying” means you have actual knowledge that, but +for the patent license, your conveying the covered work in a country, or your +recipient's use of the covered work in a country, would infringe one or more +identifiable patents in that country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or arrangement, you +convey, or propagate by procuring conveyance of, a covered work, and grant a patent +license to some of the parties receiving the covered work authorizing them to use, +propagate, modify or convey a specific copy of the covered work, then the patent +license you grant is automatically extended to all recipients of the covered work and +works based on it. + +A patent license is “discriminatory” if it does not include within the +scope of its coverage, prohibits the exercise of, or is conditioned on the +non-exercise of one or more of the rights that are specifically granted under this +License. You may not convey a covered work if you are a party to an arrangement with +a third party that is in the business of distributing software, under which you make +payment to the third party based on the extent of your activity of conveying the +work, and under which the third party grants, to any of the parties who would receive +the covered work from you, a discriminatory patent license (a) in connection with +copies of the covered work conveyed by you (or copies made from those copies), or (b) +primarily for and in connection with specific products or compilations that contain +the covered work, unless you entered into that arrangement, or that patent license +was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting any implied +license or other defenses to infringement that may otherwise be available to you +under applicable patent law. + +### 12. No Surrender of Others' Freedom. + +If conditions are imposed on you (whether by court order, agreement or otherwise) +that contradict the conditions of this License, they do not excuse you from the +conditions of this License. If you cannot convey a covered work so as to satisfy +simultaneously your obligations under this License and any other pertinent +obligations, then as a consequence you may not convey it at all. For example, if you +agree to terms that obligate you to collect a royalty for further conveying from +those to whom you convey the Program, the only way you could satisfy both those terms +and this License would be to refrain entirely from conveying the Program. + +### 13. Use with the GNU Affero General Public License. + +Notwithstanding any other provision of this License, you have permission to link or +combine any covered work with a work licensed under version 3 of the GNU Affero +General Public License into a single combined work, and to convey the resulting work. +The terms of this License will continue to apply to the part which is the covered +work, but the special requirements of the GNU Affero General Public License, section +13, concerning interaction through a network will apply to the combination as such. + +### 14. Revised Versions of this License. + +The Free Software Foundation may publish revised and/or new versions of the GNU +General Public License from time to time. Such new versions will be similar in spirit +to the present version, but may differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program specifies that +a certain numbered version of the GNU General Public License “or any later +version” applies to it, you have the option of following the terms and +conditions either of that numbered version or of any later version published by the +Free Software Foundation. If the Program does not specify a version number of the GNU +General Public License, you may choose any version ever published by the Free +Software Foundation. + +If the Program specifies that a proxy can decide which future versions of the GNU +General Public License can be used, that proxy's public statement of acceptance of a +version permanently authorizes you to choose that version for the Program. + +Later license versions may give you additional or different permissions. However, no +additional obligations are imposed on any author or copyright holder as a result of +your choosing to follow a later version. + +### 15. 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. + + + Copyright (C) + + 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 . + +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: + + Copyright (C) + 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 +<>. + +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 +<>. \ No newline at end of file diff --git a/VERSION b/VERSION index 7dea76e..9084fa2 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.0.1 +1.1.0 diff --git a/application.rb b/application.rb index b9c267c..5f64b84 100644 --- a/application.rb +++ b/application.rb @@ -1,5 +1,5 @@ #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 @@ -20,20 +20,24 @@ 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 = @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 + 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") @@ -45,7 +49,7 @@ get '/predict/modeldetails/:model' do # end #end - return haml :model_details, :layout=> false, :locals => {:model => model} + return haml :model_details, :layout=> false, :locals => {:model => model, :crossvalidations => crossvalidations} end get '/jme_help/?' do @@ -305,6 +309,12 @@ post '/predict/?' do haml :prediction 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 diff --git a/config.ru b/config.ru index 3e82e35..7ee908a 100644 --- a/config.ru +++ b/config.ru @@ -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/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/layout.haml b/views/layout.haml index a40b68c..dddf854 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"} @@ -26,7 +26,7 @@ %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 @@ -55,7 +55,7 @@ %img.share{:src=>"/images/Facebook.png"} %div.row Previous version: - %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old + %a{:href=>"http://lazar-old.in-silico.ch", :rel => "external"} lazar-old :javascript $(document).ready(function(){ $("#back-top").hide(); @@ -79,15 +79,17 @@ %p.text-muted © %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico 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"} 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..7646471 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -1,26 +1,39 @@ %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 - +%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 +47,81 @@ Source: = "Accuracy:\t" = cv.accuracy.round(3) if cv.accuracy %br + = "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 /= "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"+"2"+":" = cv.r_squared.round(3) if cv.r_squared %br /= "Confidence plot:" @@ -113,5 +131,5 @@ Source: /= "Correlation plot" /%p.plot / %img{:src=>"/corrp#{cv.id}.svg"} - + %br diff --git a/views/neighbors.haml b/views/neighbors.haml index 096e432..d9f2796 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -79,20 +79,19 @@ - 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 %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("
") : features.join("
") + = (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[:tanimoto] != nil ? neighbor[:tanimoto].to_f.round(3) : "Not enough similar compounds
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..8ae5684 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 0f3d57b..1aefe06 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -18,7 +18,6 @@ %td{:id=>"compound", :style=>"vertical-align:top;"} %p= @compound.svg %p= @compound.smiles - - mw = @compound.molecular_weight - @model_types = {} - @dbhit = {} - @predictions.each_with_index do |prediction,i| @@ -29,17 +28,20 @@ %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] - 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("
") : 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("
") : 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] + = (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) @@ -47,23 +49,30 @@ = 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:"

lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.

Classification:
Majority vote of neighbor activities weighted by similarity.

Regression:
Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.

Original publication."}} %br + = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})
#{@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 - 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)"}" + - 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 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."}} + %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) 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)} %" - -- cgit v1.2.3 From c5ca09fb039e38abd89005d49ef373cf18b79039 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 28 Nov 2016 14:13:18 +0000 Subject: bumped version;training dataset download;show warnings for batch;csv info and upload catch;code cleanup --- VERSION | 2 +- application.rb | 235 +++++++---------------------------------------- config.ru | 2 +- lazar-gui.gemspec | 2 +- views/batch.haml | 106 ++++++++++++++------- views/layout.haml | 38 +------- views/model_details.haml | 4 + views/neighbors.haml | 13 ++- views/predict.haml | 1 + views/prediction.haml | 103 +++++++++++---------- 10 files changed, 180 insertions(+), 326 deletions(-) diff --git a/VERSION b/VERSION index 9084fa2..ec63514 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.1.0 +9 diff --git a/application.rb b/application.rb index 5f64b84..eefd833 100644 --- a/application.rb +++ b/application.rb @@ -1,11 +1,6 @@ #require_relative 'helper.rb' 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) @@ -38,16 +33,6 @@ end get '/predict/modeldetails/:model' do model = OpenTox::Model::Prediction.find params[: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 @@ -56,198 +41,47 @@ get '/jme_help/?' do File.read(File.join('views','jme_help.html')) end -# get individual compound details -get '/prediction/:neighbor/details/?' do - @compound = OpenTox::Compound.new 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 - @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] - #$logger.debug "fingerprints:\t#{fingerprints}\n" - - # collect fingerprints with value 1 - @fingerprint_values = fingerprints.collect{|smarts, value| [smarts, value] if value > 0} - - # collect all features from feature_dataset - @features = feature_dataset.features.collect{|f| f } - - # search for each fingerprint in all features and collect feature values( effect, smarts, pValue ) - @fingerprint_values.each{ |fi, v| @features.each{ |f| @significant_fragments << [f[RDF::OT.effect].to_i, f[RDF::OT.smarts], f[RDF::OT.pValue]] if fi == f[RDF::OT.smarts] } } - - # pass value_map, important to interprete effect value - prediction_feature_uri = "" - model.parameters.each {|p| - if p[RDF::DC.title].to_s == "prediction_feature_uri" - prediction_feature_uri = p[RDF::OT.paramValue].object - end - } - prediction_feature = OpenTox::Feature.find prediction_feature_uri - @value_map = prediction_feature.value_map - - else #regression - feature_calc_algo = "" - model.parameters.each {|p| - if p[RDF::DC.title].to_s == "feature_calculation_algorithm" - feature_calc_algo = p[RDF::OT.paramValue].object - end - } - - @desc = [] - fingerprints = OpenTox::Algorithm::Descriptor.send( feature_calc_algo, [ @compound ], feature_dataset.features.collect{ |f| f[RDF::DC.title] } ) - fingerprints.each{|x, h| h.each{|descriptor, value| @desc << [descriptor, [value]]}} - - pc_descriptor_titles_descriptions = {} - feature_dataset.features.collect{ |f| - pc_descriptor_titles_descriptions[f[RDF::DC.title]]= f[RDF::DC.description] - } - - @desc.each{|d, v| @significant_fragments << [pc_descriptor_titles_descriptions[d], v] } - end - - haml :significant_fragments, :layout => false -end - -get '/prediction/:model_uri/:type/:neighbor/significant_fragments/?' do - @type = params[:type] - @compound = OpenTox::Compound.new params[:neighbor] - model = OpenTox::Model::Lazar.find params[:model_uri] - #$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 @@ -265,11 +99,21 @@ 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 @@ -283,7 +127,9 @@ post '/predict/?' do end end @@batch = @batch + @warnings = dataset[:warnings] dataset.delete + File.delete File.join("tmp", params[:fileselect][:filename]) return haml :batch end @@ -295,7 +141,7 @@ 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 @@ -310,17 +156,6 @@ 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/config.ru b/config.ru index 7ee908a..8f9daf5 100644 --- a/config.ru +++ b/config.ru @@ -1,4 +1,4 @@ -ENV["LAZAR_ENV"] = "development" +ENV["LAZAR_ENV"] = "production" require 'bundler' Bundler.require require File.expand_path './application.rb' diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index af5f0f9..9a43bd8 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -13,7 +13,7 @@ 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 "lazar" 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' 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("
") : 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})
#{compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("
") : prediction[:measurements].join(", ") + - else + = (type == "Regression") ? "#{prediction[:measurements].delog10} (#{unit})
#{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})
#{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
in training dataset." diff --git a/views/layout.haml b/views/layout.haml index dddf854..5ed63e8 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -29,33 +29,11 @@ %h1.media-heading lazar toxicity predictions %div.col-md-2 - %h1.media-heading + %h5 %small - %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar + [version: #{@version}] %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(); @@ -79,18 +57,6 @@ %p.text-muted © %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico 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%;"} diff --git a/views/model_details.haml b/views/model_details.haml index 7646471..3fa8c8b 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -12,6 +12,10 @@ Source: = "Training compounds:\t" = training_dataset.compounds.size %br += "Training dataset:\t" +%a{:href=>"#{to("/predict/dataset/#{training_dataset.name}")}"} + = training_dataset.name +%br %b Algorithms: %br Similarity: diff --git a/views/neighbors.haml b/views/neighbors.haml index d9f2796..32b8389 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:"Tanimoto/Jaccard similarity based on Molprint2D 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:"Tanimoto/Jaccard similarity based on Molprint2D fingerprints."}, :style=>"z-index:auto+10;"} / %th{:style =>"vertical-align:middle;"} / Supporting Information %tbody @@ -84,11 +84,14 @@ /%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[: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" + - if neighbor[:measurement].is_a?(Array) + = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10} (#{unit})
#{c.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("
") : neighbor[:measurement].join(", ") + - else + = (type == "Regression") ? "#{neighbor[:measurement].delog10} (#{unit})
#{c.mmol_to_mg(neighbor[:measurement].delog10)} #{(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%;"} = neighbor[:similarity].round(3) diff --git a/views/predict.haml b/views/predict.haml index 66006d4..9a7d0d4 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -127,6 +127,7 @@ %p %label{:for=>"fileselect"} or upload a CSV file for batch predictions + %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"} diff --git a/views/prediction.haml b/views/prediction.haml index 2454aca..b090be5 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -18,7 +18,6 @@ %td{:id=>"compound", :style=>"vertical-align:top;"} %p= @compound.svg %p= @compound.smiles - -#- mw = @compound.molecular_weight - @model_types = {} - @dbhit = {} - @predictions.each_with_index do |prediction,i| @@ -28,62 +27,66 @@ %td{:style=>"vertical-align:top;white-space:nowrap;"} %b{:class => "title"} = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})" - %p - - if prediction[:warning] =~ /\b(identical)\b/i - - @dbhit[i] = true + + / check for prediction + - if prediction[:neighbors].size > 0 %p - /TODO combine with regular view, if prediction value is present - %b Measured activity: - - p prediction[:value] - - if prediction[:value].is_a?(Array) - = (type == "Regression") ? prediction[:value].collect{|value| "#{value} (#{unit}) , #{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("
") : prediction[:value].join(", ") - - else - = (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) + / show model type (classification|regression) %b Type: = type - %br - %b Prediction: - / prediction popover - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"

lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.

Classification:
Majority vote of neighbor activities weighted by similarity.

Regression:
Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.

Original publication."}} - %br - = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})
#{@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 - - 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? + %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} (#{unit})
#{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("
") : prediction[:measurements].join(", ") + - else + = (type == "Regression") ? "#{prediction[:measurements].delog10} (#{unit})
#{@compound.mmol_to_mg(prediction[:measurements].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements] + - else - %b Probability: - - unless prediction[:probabilities].nil? + - @dbhit[i] = false + + / show prediction + %p + %b Prediction: + / prediction popover + -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"

lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.

Classification:
Majority vote of neighbor activities weighted by similarity.

Regression:
Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.

Original publication."}} + %br + = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})
#{@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]) + / prediction interval 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 - = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}" + = interval.nil? ? "--" : "#{interval[1].delog10} - #{interval[0].delog10} (#{unit})" %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", :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 + = "#{@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 + = "#{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."}} + + / 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 -- cgit v1.2.3 From 437b78faf4bcd820ea3193da18abf6b71eda8153 Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 30 Nov 2016 12:50:53 +0000 Subject: minor fix --- .gitignore | 1 - lazar-gui.gemspec | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index a0459cb..49b161f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,2 @@ Gemfile.lock .sass-cache/ -tmp/* diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index 9a43bd8..6f58687 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -19,7 +19,7 @@ Gem::Specification.new do |s| 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 "unicorn" s.post_install_message = %q{ Service cmds: -- cgit v1.2.3 From 725b6d27302ebacda9ff2900b4c55bdbf1a73d06 Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 7 Dec 2016 06:37:45 +0000 Subject: removed required gem versions --- lazar-gui.gemspec | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index af5f0f9..4d5526b 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" + 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: -- cgit v1.2.3 From 55bf06381a42c9bb1e1e991e990f5d6e90c8e33e Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 7 Dec 2016 12:07:13 +0000 Subject: rebuild code for public release;prepared to work with lazar v1.0.0;reintroduced compound details --- VERSION | 2 +- application.rb | 27 ++++++- config.ru | 2 +- helper.rb | 215 -------------------------------------------------- views/details.haml | 6 +- views/layout.haml | 37 ++++++++- views/neighbors.haml | 4 +- views/predict.haml | 12 +-- views/prediction.haml | 22 +++--- 9 files changed, 82 insertions(+), 245 deletions(-) diff --git a/VERSION b/VERSION index ec63514..9084fa2 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -9 +1.1.0 diff --git a/application.rb b/application.rb index eefd833..4eb4a36 100644 --- a/application.rb +++ b/application.rb @@ -24,19 +24,33 @@ get '/?' do end get '/predict/?' do - @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] + 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, :crossvalidations => crossvalidations} end +# get individual compound details +get '/prediction/:neighbor/details/?' do + @compound = OpenTox::Compound.find params[:neighbor] + @smiles = @compound.smiles + 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 + get '/jme_help/?' do File.read(File.join('views','jme_help.html')) end @@ -121,7 +135,7 @@ 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 @@ -148,7 +162,7 @@ post '/predict/?' do @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 @@ -156,6 +170,11 @@ post '/predict/?' do end end +get '/license' do + @license = RDiscount.new(File.read("LICENSE.md")).to_html + haml :license, :layout => false +end + get '/style.css' do headers 'Content-Type' => 'text/css; charset=utf-8' scss :style diff --git a/config.ru b/config.ru index 8f9daf5..ad609be 100644 --- a/config.ru +++ b/config.ru @@ -1,4 +1,4 @@ -ENV["LAZAR_ENV"] = "production" +ENV["LAZAR_ENV"] = "development"#"production" require 'bundler' Bundler.require require File.expand_path './application.rb' diff --git a/helper.rb b/helper.rb index caa1923..54dbd5e 100644 --- a/helper.rb +++ b/helper.rb @@ -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 += "

    \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 += "
  • \n" - out += endpoint_level(endpointname, level + 1) - out += "
    • \n" - end - out += "
\n" if results.size > 0 - return out - end - - def endpoint_selection() - out = " \n -
\n" - out += "Please select:\n" - out += endpoint_level - js = "" - out += "
\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/views/details.haml b/views/details.haml index bb8250d..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 diff --git a/views/layout.haml b/views/layout.haml index 5ed63e8..62a224b 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -29,11 +29,30 @@ %h1.media-heading lazar toxicity predictions %div.col-md-2 - %h5 + %h1.media-heading %small - [version: #{@version}] + %a{:href=>"https://nano-lazar.in-silico.ch", :rel=>"external"} 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=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", :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", :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", :rel=>"external", :title=>"Share on Facebook"} + %img.share{:src=>"/images/Facebook.png"} :javascript $(document).ready(function(){ $("#back-top").hide(); @@ -57,7 +76,19 @@ %p.text-muted © %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico 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/neighbors.haml b/views/neighbors.haml index 32b8389..a608c4d 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -81,8 +81,8 @@ / 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["_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 / Measured Activity diff --git a/views/predict.haml b/views/predict.haml index 9a7d0d4..b7a4087 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -125,12 +125,12 @@ %br %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'} %p - %label{:for=>"fileselect"} - or upload a CSV file for batch predictions - %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"} + -#%label{:for=>"fileselect"} + or upload a CSV file for batch predictions (disabled in public version) + -#%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"} %fieldset#middle.well %h2 2. Select one or more endpoints diff --git a/views/prediction.haml b/views/prediction.haml index b090be5..362f006 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 @@ -16,7 +9,8 @@ %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 - @model_types = {} - @dbhit = {} @@ -57,7 +51,7 @@ %p %b Prediction: / prediction popover - -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"

lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.

Classification:
Majority vote of neighbor activities weighted by similarity.

Regression:
Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.

Original publication."}} + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"

lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.

Classification:
Majority vote of neighbor activities weighted by similarity.

Regression:
Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.

Original publication."}} %br = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})
#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] @@ -67,20 +61,20 @@ %b 95% Prediction interval: - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval]) / prediction interval 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."}} + %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} - #{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: + / probability popover + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :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."}} - 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."}} / show warnings %p @@ -94,4 +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 -- cgit v1.2.3 From cb2ad5835eae10c85ee426102b2a9bf165c5c848 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 20 Dec 2016 16:25:27 +0000 Subject: result values round by signif(n);set dependent lazar gem version --- lazar-gui.gemspec | 2 +- views/model_details.haml | 30 ++++++++++++++++-------------- views/neighbors.haml | 4 ++-- views/prediction.haml | 16 ++++++++-------- 4 files changed, 27 insertions(+), 25 deletions(-) diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index 4d5526b..f37b512 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -13,7 +13,7 @@ Gem::Specification.new do |s| s.rubyforge_project = "lazar-gui" s.files = `git ls-files`.split("\n") - s.add_runtime_dependency "lazar" + s.add_runtime_dependency "lazar", "= 1.0.0" s.add_runtime_dependency "gem-path" s.add_runtime_dependency "sinatra" s.add_runtime_dependency "rdiscount" diff --git a/views/model_details.haml b/views/model_details.haml index 3fa8c8b..5c3aa4f 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -10,7 +10,7 @@ Source: %br - 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}")}"} @@ -53,18 +53,20 @@ Descriptors: %br = "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 - %br - = "True negative rate:\t" - = cv.true_rate["inactive"].round(3) if cv.true_rate - %br - = "Positive predictive value:\t" - = cv.predictivity["active"].round(3) if cv.predictivity - %br - = "Negative predictive value:\t" - = cv.predictivity["inactive"].round(3) if cv.predictivity + - 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 - ["confusion_matrix", "weighted_confusion_matrix"].each_with_index do |matrix,idx| %b= (idx == 0 ? "Confusion Matrix" : "Weighted Confusion Matrix") @@ -136,4 +138,4 @@ Descriptors: /%p.plot / %img{:src=>"/corrp#{cv.id}.svg"} -%br +%br diff --git a/views/neighbors.haml b/views/neighbors.haml index a608c4d..2f0b3d7 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -88,9 +88,9 @@ / Measured Activity %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"} - if neighbor[:measurement].is_a?(Array) - = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10} (#{unit})
#{c.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("
") : neighbor[:measurement].join(", ") + = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10.signif(3)} (#{unit})
#{c.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("
") : neighbor[:measurement].join(", ") - else - = (type == "Regression") ? "#{neighbor[:measurement].delog10} (#{unit})
#{c.mmol_to_mg(neighbor[:measurement].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement] + = (type == "Regression") ? "#{neighbor[:measurement].delog10.signif(3)} (#{unit})
#{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%;"} diff --git a/views/prediction.haml b/views/prediction.haml index 362f006..1b8d38d 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -40,9 +40,9 @@ %b Measured activity: %br - if prediction[:measurements].is_a?(Array) - = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10} (#{unit})
#{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("
") : prediction[:measurements].join(", ") + = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{unit})
#{@compound.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("
") : prediction[:measurements].join(", ") - else - = (type == "Regression") ? "#{prediction[:measurements].delog10} (#{unit})
#{@compound.mmol_to_mg(prediction[:measurements].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements] + = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{unit})
#{@compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements] - else - @dbhit[i] = false @@ -53,7 +53,7 @@ / 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:"

lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.

Classification:
Majority vote of neighbor activities weighted by similarity.

Regression:
Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.

Original publication."}} %br - = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})
#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] + = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)} (#{unit})
#{@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 @@ -63,18 +63,18 @@ / 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} - #{interval[0].delog10} (#{unit})" + = interval.nil? ? "--" : "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)} (#{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? + = "#{@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=>"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."}} + %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]}" + = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0].signif(3)}" %br - = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}" + = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1].signif(3)}" / show warnings %p -- cgit v1.2.3 From e6b8488b757f1d6036fd74b75f44d8c75ed3779f Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 16 Jan 2017 16:53:13 +0000 Subject: issue fixes;added faq --- FAQ.md | 39 +++++++++++------------------- VERSION | 2 +- application.rb | 5 ++++ views/faq_layout.haml | 67 --------------------------------------------------- views/layout.haml | 11 +++++---- views/neighbors.haml | 8 +++++- views/predict.haml | 5 ++-- 7 files changed, 36 insertions(+), 101 deletions(-) delete mode 100644 views/faq_layout.haml diff --git a/FAQ.md b/FAQ.md index 73fec91..2530968 100644 --- a/FAQ.md +++ b/FAQ.md @@ -1,29 +1,18 @@ -Frequently Asked Questions -========================== -
-####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. diff --git a/VERSION b/VERSION index 9084fa2..524cb55 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.1.0 +1.1.1 diff --git a/application.rb b/application.rb index 4eb4a36..fa5df0a 100644 --- a/application.rb +++ b/application.rb @@ -175,6 +175,11 @@ get '/license' do haml :license, :layout => false end +get '/faq' do + @faq = RDiscount.new(File.read("FAQ.md")).to_html + haml :faq, :layout => false +end + get '/style.css' do headers 'Content-Type' => 'text/css; charset=utf-8' scss :style 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 Lazar 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"} in silico 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 62a224b..dc83956 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -36,15 +36,16 @@ %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 + %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", :rel=>"external", :title=>"Share on Google+"} diff --git a/views/neighbors.haml b/views/neighbors.haml index 2f0b3d7..18c23f8 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -3,6 +3,11 @@ / align single prediction to endpoint ; / display preordered in table view ; +:javascript + $(document).ready(function(){ + addExternalLinks(); + }); + %div.results %h3 Neighbors: / tabs div @@ -35,6 +40,7 @@ / presort by similarity ; :javascript $(document).ready(function(){ + addExternalLinks(); $("table##{j+1}").tablesorter({ debug: false, theme: "bootstrap", @@ -70,7 +76,7 @@ %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=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"Tanimoto/Jaccard similarity based on Molprint2D 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:"Tanimoto/Jaccard similarity based on Molprint2D fingerprints."}, :style=>"z-index:auto+10;"} / %th{:style =>"vertical-align:middle;"} / Supporting Information %tbody diff --git a/views/predict.haml b/views/predict.haml index b7a4087..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 @@ -130,7 +130,8 @@ -#%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=>"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 -- cgit v1.2.3