From 3935e9bee66fbfff4f35365eb9cff8c79f5fadd8 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 29 Oct 2015 10:09:13 +0000 Subject: patch merge --- application.rb | 14 ++++++++------ views/batch.haml | 3 +-- views/neighbors.haml | 4 ++-- views/predict.haml | 2 +- 4 files changed, 12 insertions(+), 11 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/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? diff --git a/views/predict.haml b/views/predict.haml index 9863cd9..8ab9ee0 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 dbb60a158ccb84f730089c5b0f61032c169dd92e Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 29 Oct 2015 12:54:15 +0000 Subject: revert last change after fix in compound lib --- 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 1d6588b35b4ffff16717e24b42a0d396d5347f95 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 26 Jan 2016 12:53:40 +0000 Subject: batch merge --- application.rb | 23 ++++++++++++++++++----- views/batch.haml | 15 +++++++++------ views/neighbors.haml | 21 ++++++++++++++++++--- views/predict.haml | 1 - views/prediction.haml | 14 +++++++++----- 5 files changed, 54 insertions(+), 20 deletions(-) diff --git a/application.rb b/application.rb index 229f3a1..fc7e415 100644 --- a/application.rb +++ b/application.rb @@ -202,21 +202,34 @@ get '/predict/?:csv?' do model = array[0] prediction = array[1] compound = key.smiles + mw = key.molecular_weight endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" if prediction[:confidence] == "measured" - type = "" - pred = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : 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}" : 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 ec987c4..9bfa67e 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 @@ -32,10 +33,13 @@ %p - if prediction[:confidence] == "measured" %p - / TODO fix scientific notation from database - %b Measured activity: - = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : 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) @@ -43,8 +47,7 @@ = model.model.class.to_s.match("Classification") ? "Classification" : "Regression" %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..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 @@ -65,9 +78,11 @@ /%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); '%.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/predict.haml b/views/predict.haml index 8ab9ee0..010ed12 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -125,7 +125,6 @@ %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 diff --git a/views/prediction.haml b/views/prediction.haml index ef0c5db..33e9ec5 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| @@ -30,10 +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})" : 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); '%.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])} (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) @@ -41,8 +46,7 @@ = 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])} (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 9eb9fd8ab470d6c44c70e0af0808204bdda2b161 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 17 Mar 2016 11:28:18 +0000 Subject: snapshot, works only with png plots --- application.rb | 12 ++++++++++++ views/model_details.haml | 24 ++++++++++++------------ views/style.scss | 9 +++++++++ 3 files changed, 33 insertions(+), 12 deletions(-) diff --git a/application.rb b/application.rb index fc7e415..a4dc7c4 100644 --- a/application.rb +++ b/application.rb @@ -31,6 +31,18 @@ end get '/predict/modeldetails/:model' do model = OpenTox::Model::Prediction.find params[:model] + crossvalidations = model.crossvalidations + confidence_plots = crossvalidations.collect{|cv| [cv.id, cv.confidence_plot]} + confidence_plots.each do |confp| + File.open(File.join('public', "confp#{confp[0]}.png"), 'w'){|file| file.write(confp[1])} unless File.exists? File.join('public', "confp#{confp[0]}.png") + 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]}.png"), 'w'){|file| file.write(corrp[1])} unless File.exists? File.join('public', "corrp#{corrp[0]}.png") + end + end + return haml :model_details, :layout=> false, :locals => {:model => model} end diff --git a/views/model_details.haml b/views/model_details.haml index e5886e7..04cc0f0 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -97,10 +97,9 @@ Source: -#= "Confusion Matrix:\t" -#= cv.confusion_matrix %br - -#%p - = "Confidence plot:" - -#%p{:id=>"confp#{cv.id}", :style=>"transform:scale(0.5);margin-left:-30%;margin-top:-30%;padding:0;"} - = cv.confidence_plot + = "Confidence plot:" + %p.plot + %img{:src=>"confp#{cv.id}.png"} - if model.regression? %br = "Root mean squared error:\t" @@ -117,12 +116,13 @@ Source: %br = "R square:\t" = cv.r_squared.round(3) if cv.r_squared - -#%p - = "Correlation plot" - -#%p{:id=>"corrp#{cv.id}", :style=>"transform:scale(0.5);margin-left:-30%;margin-top:-30%;margin-bottom:0;padding:0;"} - =cv.correlation_plot - -#%p - = "Confidence plot:" - -#%p{:id=>"confp#{cv.id}", :style=>"transform:scale(0.5);margin-left:-30%;margin-top:-30%;margin-bottom:0;padding:0;"} - = cv.confidence_plot + %br + = "Confidence plot:" + %p.plot + %img{:src=>"/confp#{cv.id}.png"} + %br + = "Correlation plot" + %p.plot + %img{:src=>"/corrp#{cv.id}.png"} + %br diff --git a/views/style.scss b/views/style.scss index 9a3c9df..a0502b5 100644 --- a/views/style.scss +++ b/views/style.scss @@ -16,3 +16,12 @@ h4.head-back, h5.head-back{ height: 5em; } } +img { + max-width: 100%; + max-height: 100%; +} + +.plot { + height: 300px; + width: 300px; +} -- cgit v1.2.3 From 510822b13d48344ffe4e047a4415ebdb218dadc0 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 24 Mar 2016 19:41:37 +0000 Subject: updated for latest lazar changes; introduced 95% prediction interval --- application.rb | 20 ++++++++++---------- views/model_details.haml | 29 ++++++++++------------------- views/neighbors.haml | 31 +++++++++++++++++++++---------- views/prediction.haml | 11 ++++++++--- 4 files changed, 49 insertions(+), 42 deletions(-) diff --git a/application.rb b/application.rb index a4dc7c4..6c6a73f 100644 --- a/application.rb +++ b/application.rb @@ -32,16 +32,16 @@ end get '/predict/modeldetails/:model' do model = OpenTox::Model::Prediction.find params[:model] crossvalidations = model.crossvalidations - confidence_plots = crossvalidations.collect{|cv| [cv.id, cv.confidence_plot]} - confidence_plots.each do |confp| - File.open(File.join('public', "confp#{confp[0]}.png"), 'w'){|file| file.write(confp[1])} unless File.exists? File.join('public', "confp#{confp[0]}.png") - 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]}.png"), 'w'){|file| file.write(corrp[1])} unless File.exists? File.join('public', "corrp#{corrp[0]}.png") - end - end + #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} end diff --git a/views/model_details.haml b/views/model_details.haml index 04cc0f0..34e86ac 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -36,9 +36,6 @@ 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"] %br @@ -97,32 +94,26 @@ Source: -#= "Confusion Matrix:\t" -#= cv.confusion_matrix %br - = "Confidence plot:" - %p.plot - %img{:src=>"confp#{cv.id}.png"} + /= "Confidence plot:" + /%p.plot + / %img{:src=>"confp#{cv.id}.svg"} - if model.regression? %br = "Root mean squared error:\t" = cv.rmse.round(3) if cv.rmse %br - = "Weighted root mean squared error:\t" - = cv.weighted_rmse.round(3) if cv.weighted_rmse - %br = "Mean absolute error:\t" = cv.mae.round(3) if cv.mae - %br - = "Weighted mean absolute error:\t" - = cv.weighted_mae.round(3) if cv.weighted_mae %br = "R square:\t" = cv.r_squared.round(3) if cv.r_squared %br - = "Confidence plot:" - %p.plot - %img{:src=>"/confp#{cv.id}.png"} - %br - = "Correlation plot" - %p.plot - %img{:src=>"/corrp#{cv.id}.png"} + /= "Confidence plot:" + /%p.plot + / %img{:src=>"/confp#{cv.id}.svg"} + /%br + /= "Correlation plot" + /%p.plot + / %img{:src=>"/corrp#{cv.id}.svg"} %br diff --git a/views/neighbors.haml b/views/neighbors.haml index 6001605..6011a6d 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -9,7 +9,17 @@ #tabs %ul.nav.nav-tabs.nav-justified{:id=>"neighborTabs", :role=>"tablist"} / each model a tab head ; + / hash for predictionFeature + - predictionFeature = {} - @models.each_with_index do |model,i| + / get predictionFeature type + - m = Model::Lazar.find model.model_id.to_s + - predFeature = Feature.find m.prediction_feature_id.to_s + / define feature type (numeric : nominal) + - predFeatureType = (predFeature.numeric? ? "numeric" : "nominal") + / use prediction feature id for neighbor compound features + - predFeatureId = m.prediction_feature_id.to_s + - predictionFeature[i] = {"id" => predFeatureId, "type" => predFeatureType} %li{:class => ("active" if i == 0)} %a{:href => "#results_#{i+1}", :id => "linkTab#{i+1}", data: {toggle:"tab"}} = "#{model.endpoint} (#{model.species})" @@ -29,7 +39,7 @@ debug: false, theme: "bootstrap", headerTemplate: '{content} {icon}', - widgets: ['zebra', 'columns', 'uitheme', 'stickyHeaders'], + widgets: ['columns', 'uitheme', 'stickyHeaders'], widgetOptions: { stickyHeaders_attachTo : '.tab-content', stickyHeaders : '', @@ -74,19 +84,20 @@ - prediction[:neighbors].uniq.each_with_index do |neighbor,count| %tr / Compound + - c = Compound.find(neighbor["_id"]) %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"} - /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}} - %p= Compound.find(neighbor[0]).svg - %p= Compound.find(neighbor[0]).smiles - - c = Compound.find(neighbor[0]) - //- mw = c.molecular_weight - / Measured Activity + /%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 %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"} - = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("
") : neighbor[2].join(", ") - / Similarity + - 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} (mg/kg_bw/day)"}.join("
") : features.join("
") + / Similarity = tanimoto %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"} / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset? - = neighbor[1] != nil ? neighbor[1].round(2) : "Not enough similar compounds
in training dataset." + = neighbor[:tanimoto] != nil ? neighbor[:tanimoto].to_f.round(3) : "Not enough similar compounds
in training dataset." - else %span.btn.btn-default.disabled diff --git a/views/prediction.haml b/views/prediction.haml index 33e9ec5..aeaafdc 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| @@ -51,8 +51,13 @@ / %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 / TODO probability - %b Confidence: - = prediction[:confidence].round(2) + - if type == "Regression" + %b 95% Prediction interval: + - interval = prediction[:prediction_interval].collect{|i| i.round(2)} + = interval + - else + %b Confidence: + = prediction[:confidence].round(2) unless prediction[:confidence].nil? / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}} %p /TODO add tooltip for significant ftagments and descriptors -- cgit v1.2.3 From d70373fb5a35740f1246d9a37ce1567e899c8a1a Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 31 Mar 2016 10:53:45 +0200 Subject: catch empty pred interval --- views/prediction.haml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/views/prediction.haml b/views/prediction.haml index aeaafdc..f99df75 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -53,7 +53,7 @@ / TODO probability - if type == "Regression" %b 95% Prediction interval: - - interval = prediction[:prediction_interval].collect{|i| i.round(2)} + - interval = prediction[:prediction_interval].nil? ? "[ - - ]" : prediction[:prediction_interval].collect{|i| i.round(2)} = interval - else %b Confidence: -- cgit v1.2.3 From 4a108bd930a367cad06b3ef0208c7b7760753329 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 12 Apr 2016 13:22:57 +0200 Subject: use lazar gem --- Gemfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile b/Gemfile index 736527c..8517fde 100644 --- a/Gemfile +++ b/Gemfile @@ -3,4 +3,4 @@ gemspec gem "sinatra" gem "haml" gem "sass" -gem "lazar", :path => "../lazar" +gem "lazar"#, :path => "../lazar" -- cgit v1.2.3 From df8ed98fcc052da2641c26897a8dd0592f274e53 Mon Sep 17 00:00:00 2001 From: gebele Date: Fri, 15 Apr 2016 09:59:43 +0000 Subject: reactivated info buttons; changed unit for fish; introduced FAQ --- FAQ.md | 29 ++++++++++++++++++++++ README | 10 -------- README.md | 15 ++++++++++++ application.rb | 6 +++++ lazar-gui.gemspec | 4 +-- views/faq.haml | 2 ++ views/faq_layout.haml | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++ views/layout.haml | 5 +++- views/neighbors.haml | 7 +++--- views/prediction.haml | 23 ++++++++++-------- views/style.scss | 12 +++++++++ 11 files changed, 154 insertions(+), 26 deletions(-) create mode 100644 FAQ.md delete mode 100644 README create mode 100644 README.md create mode 100644 views/faq.haml create mode 100644 views/faq_layout.haml diff --git a/FAQ.md b/FAQ.md new file mode 100644 index 0000000..73fec91 --- /dev/null +++ b/FAQ.md @@ -0,0 +1,29 @@ +Frequently Asked Questions +========================== +
+####How does this prediction works? +> + +####You talk about significant fragments. Where can I find them? +> We will show up those significant fragments in a further version. + +####What is endpoint details about? +> You get the source from where we took compounds for the endpoint. The type and the number of compounds we used. + +####What is three times independent validation about? +> + +####Do you consider providing plots for the validation results? +> In a further version we will show up confidence and correlation plots. + +####What does 'Not enough similar compounds in training dataset' mean? +> Lazar uses neighbors from the training dataset of the endpoint to predict your compound. If there are not enough neighbors for Lazar it is not possible to make a prediction. + +####Is there a minimum number of necessary neighbors to make a prediction? +> + +####How can I activate the 'batch prediction' option? +> Please contact us directly via [mail](mailto:support@in-silico.ch). + +####Not the right answers for me. Is there a way to contact you or report problems. +> You can always ask your questions via [mail](mailto:support@in-silico.ch). If you run into problems with the GUI please post your issue [here](https://github.com/opentox/lazar-gui/issues). If you would like to post any other issue e.g. about an expected prediction result please use this [form](https://github.com/opentox/lazar/issues). diff --git a/README b/README deleted file mode 100644 index f162be7..0000000 --- a/README +++ /dev/null @@ -1,10 +0,0 @@ -IST Software&Services GUI - -installation: -- bundle install -- ~/.opentox/config/lazar-gui.rb (point to services) - -usage: --start services --run 'unicorn -D' --visit 'localhost:8080' diff --git a/README.md b/README.md new file mode 100644 index 0000000..2142dd5 --- /dev/null +++ b/README.md @@ -0,0 +1,15 @@ +IST Software&Services GUI +========================= + +Installation: +------------- + bundle install + +Usage: +------ + sudo /etc/init.d/mongod start + unicorn -D + +Visit: +------ + http://localhost:8080 diff --git a/application.rb b/application.rb index 6c6a73f..cebe4f2 100644 --- a/application.rb +++ b/application.rb @@ -1,4 +1,5 @@ require_relative 'helper.rb' +require 'rdiscount' include OpenTox #require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb") # until added to ot-tools @@ -304,6 +305,11 @@ post '/predict/?' do end end +get '/faq' do + @faq = RDiscount.new(File.read("FAQ.md")).to_html + haml :faq, :layout => :faq_layout +end + get '/style.css' do headers 'Content-Type' => 'text/css; charset=utf-8' scss :style diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index dd852a0..db29827 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -15,9 +15,9 @@ Gem::Specification.new do |s| s.files = `git ls-files`.split("\n") s.required_ruby_version = '>= 1.9.2' - #s.add_runtime_dependency "opentox-server" - s.add_runtime_dependency "lazar" + s.add_runtime_dependency "lazar", "~> 0.9.3" 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" diff --git a/views/faq.haml b/views/faq.haml new file mode 100644 index 0000000..818b96a --- /dev/null +++ b/views/faq.haml @@ -0,0 +1,2 @@ +%div.well.faq + = @faq diff --git a/views/faq_layout.haml b/views/faq_layout.haml new file mode 100644 index 0000000..a9b6664 --- /dev/null +++ b/views/faq_layout.haml @@ -0,0 +1,67 @@ +!!! +%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"} + %head + %meta{'charset'=>"utf-8"} + %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"} + %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"} + %title Lazar GUI FAQ + %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'} + %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"} + %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"} + %link{:rel=>'stylesheet', :href=>"#{'/css/theme.bootstrap.min.css'}"} + %link{ :href=>"/style.css", :rel=>"stylesheet"} + %link{ :href=>"/stylesheets/jquery-ui.css", :rel=>"stylesheet"} + %script{:src=>"/javascripts/jquery-1.11.2.min.js"} + %script{:src=>"/javascripts/bootstrap.min.js"} + %script{ :src=>"/javascripts/lazar-gui.js"} + %body + %noscript + %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"} + Your web browser must have JavaScript enabled in order for this application to display correctly. + %header.page-header + %div.row + %div.col-md-2 + %a{:href=> to("/predict")} + %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"} + %div.col-md-10 + %h1.media-heading{:style=>"margin: 0 0 0 1em;display:inline;"} Lazar GUI + A Graphical User Interface for the 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 60f2bb3..46d326d 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -16,7 +16,7 @@ %script{:src=>"/javascripts/jquery.tablesorter.min.js"} %script{:src=>"/javascripts/jquery.tablesorter.widgets.js"} %script{ :src=>"/javascripts/lazar-gui.js"} - %body{:style=>"background-color:#E7E7E7"} + %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. @@ -27,6 +27,9 @@ %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"} %div.col-md-8 %h1.media-heading{:style=>"margin: 0 0 0 1em;"} Lazar Toxicity Predictions + %div.col-md-2 + %a.btn.btn-info{:href=> to("/faq"), :rel => "external"} + FAQ %div.container-fluid :javascript diff --git a/views/neighbors.haml b/views/neighbors.haml index 6011a6d..c94331a 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -75,12 +75,13 @@ %tr %td %td{:style=>"font-size:x-small;padding:0px;"} - / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", data: {toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"} + %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;"} %td{:style=>"font-size:x-small;padding:0px;"} - / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", data: {toggle:"popover", placement:"auto", html:"true", content:"LAZAR calculates activity specific similarities based on the presence of statistically significant fragments. This procedure will
  • consider only those parts of a chemical structure that are relevant for a particular endpoint
  • ignore inert parts of the structure
  • lead to different similarities, depending on the toxic endpoint Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.
"}, :style=>"z-index:auto+10;"} + %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates activity specific similarities based on the presence of statistically significant fragments. This procedure will
  • consider only those parts of a chemical structure that are relevant for a particular endpoint
  • ignore inert parts of the structure
  • lead to different similarities, depending on the toxic endpoint Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.
"}, :style=>"z-index:auto+10;"} / %td %tbody - type = @model_types[j] + - unit = @models[j].unit - prediction[:neighbors].uniq.each_with_index do |neighbor,count| %tr / Compound @@ -93,7 +94,7 @@ / Measured Activity = compound.features %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} (mg/kg_bw/day)"}.join("
") : features.join("
") + = (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("
") / 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? diff --git a/views/prediction.haml b/views/prediction.haml index f99df75..89c33d6 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -24,6 +24,7 @@ - @predictions.each_with_index do |prediction,i| - type = @models[i].model.class.to_s.match("Classification") ? "Classification" : "Regression" - @model_types[i] = type + - unit = @models[i].unit %td{:style=>"vertical-align:top;white-space:nowrap;"} %b{:class => "title"} = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})" @@ -34,9 +35,9 @@ %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); '%.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 + " (#{unit})"+"|#{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("
") : prediction[:value].join(", ") - else - = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value] + = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] %p %b Compound is part of the training dataset - elsif prediction[:neighbors].size > 0 @@ -46,27 +47,29 @@ = type %br %b Prediction: - = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} (mg/kg_bw/day)" : prediction[:value] - / TODO update description - / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using Please keep in mind that predictions are based on the measured activities of neighbors."}} + = (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. + %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", 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 - / TODO probability - if type == "Regression" %b 95% Prediction interval: - interval = prediction[:prediction_interval].nil? ? "[ - - ]" : prediction[:prediction_interval].collect{|i| i.round(2)} - = interval + = "[#{interval[0]} (#{unit}), #{interval[1]} (#{unit})]" + / 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:"A prediction interval (wikipedia) is an estimate of an interval in which future observations will fall, with a certain probability, given what has already been observed."}} - else %b Confidence: = prediction[:confidence].round(2) unless prediction[:confidence].nil? - / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}} + / 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."}} %p /TODO add tooltip for significant ftagments and descriptors / - if @model_type[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) / Significant fragments: - / %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments + / %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments / - if @model_type[i] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) / Descriptors - / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors + / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors / %p %p - else diff --git a/views/style.scss b/views/style.scss index a0502b5..70c8035 100644 --- a/views/style.scss +++ b/views/style.scss @@ -1,3 +1,6 @@ +body { + background-color:#E7E7E7; +} table.table-borderless tbody tr td{ border-top: none; } @@ -25,3 +28,12 @@ img { height: 300px; width: 300px; } +.faq { + text-align: block; + margin-left:15%; + margin-right:15%; + margin-top:2%; +} +.faq h1 { + text-align: center; +} -- cgit v1.2.3 From 512458e2489c8cc12a9d539d8895c1802d7b081a Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 20 Apr 2016 14:12:03 +0000 Subject: adopted changes from CH on the master branch --- views/neighbors.haml | 4 +++- views/prediction.haml | 1 + 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/views/neighbors.haml b/views/neighbors.haml index c94331a..3014255 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -75,9 +75,11 @@ %tr %td %td{:style=>"font-size:x-small;padding:0px;"} + / 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;"} %td{:style=>"font-size:x-small;padding:0px;"} - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates activity specific similarities based on the presence of statistically significant fragments. This procedure will
  • consider only those parts of a chemical structure that are relevant for a particular endpoint
  • ignore inert parts of the structure
  • lead to different similarities, depending on the toxic endpoint Similarities of 1 may be encountered even for structurally dissimilar compounds, because inert parts are ignored.
"}, :style=>"z-index:auto+10;"} + / 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;"} / %td %tbody - type = @model_types[j] diff --git a/views/prediction.haml b/views/prediction.haml index 89c33d6..4a2877e 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -49,6 +49,7 @@ %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 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 - if type == "Regression" -- cgit v1.2.3 From 5c40dfe6ca17d318a0ec0dfcfe07b174f4d71e59 Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 20 Apr 2016 14:19:02 +0000 Subject: edited model details --- views/model_details.haml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/views/model_details.haml b/views/model_details.haml index 34e86ac..1be75e7 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -4,21 +4,19 @@ Source: %a{:href=>model.source, :target=>"external"} = model.source %br -= "Algorithm:\tLAZAR" -%br - model.classification? ? type = "Classification" : type = "Regression" = "Type:\t" = type %br - training_dataset = OpenTox::Dataset.find model.training_dataset.id -= "Training dataset:\t" -= training_dataset.source.split("/").last -%br = "Training compounds:\t" = training_dataset.compounds.size %p -%b Crossvalidation (3 independent): +- if type == "Classification" + %b Independent crossvalidations: +- else + %b Independent crossvalidations (-log10 transformed): %div.row{:id=>"validations#{model.id}", :style=>"background-color:#f5f5f5;"} - model.crossvalidations.each do |crossvalidation| %span.col-xs-4.col-sm-4.col-md-4.col-lg-4 -- cgit v1.2.3 From 7759519665408673e2ab1bfd8d32a84168c2ee34 Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 20 Apr 2016 14:39:22 +0000 Subject: adjusted prediction intervall info; units ; depiction --- views/prediction.haml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/views/prediction.haml b/views/prediction.haml index 4a2877e..5265504 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -47,7 +47,7 @@ = 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] + = (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 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."}} @@ -55,9 +55,10 @@ - if type == "Regression" %b 95% Prediction interval: - interval = prediction[:prediction_interval].nil? ? "[ - - ]" : prediction[:prediction_interval].collect{|i| i.round(2)} - = "[#{interval[0]} (#{unit}), #{interval[1]} (#{unit})]" + %br + = "[#{interval[0]} - #{interval[1]}] (#{unit}), [#{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])}] (mg/L)" / 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:"A prediction interval (wikipedia) is an estimate of an interval in which future observations will fall, with a certain probability, given what has already been observed."}} + %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."}} - else %b Confidence: = prediction[:confidence].round(2) unless prediction[:confidence].nil? -- cgit v1.2.3 From 48738e50ab34768cccfc770d3010c4f055bd76eb Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 20 Apr 2016 14:44:57 +0000 Subject: updated similarity info; changed delimiter --- views/neighbors.haml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/views/neighbors.haml b/views/neighbors.haml index 3014255..2edc3ab 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -79,7 +79,7 @@ %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;"} %td{:style=>"font-size:x-small;padding:0px;"} / 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=>"#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;"} / %td %tbody - type = @model_types[j] @@ -96,7 +96,7 @@ / Measured Activity = compound.features %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("
") + = (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("
") / 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? -- cgit v1.2.3 From 9d6043aef3836e0678942dccda2d8eeda0dc17b4 Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 20 Apr 2016 14:49:21 +0000 Subject: keep back faq --- application.rb | 4 ++-- views/layout.haml | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/application.rb b/application.rb index cebe4f2..7b774bc 100644 --- a/application.rb +++ b/application.rb @@ -304,12 +304,12 @@ post '/predict/?' do haml :prediction end 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/views/layout.haml b/views/layout.haml index 46d326d..a49238f 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -27,9 +27,9 @@ %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"} %div.col-md-8 %h1.media-heading{:style=>"margin: 0 0 0 1em;"} Lazar Toxicity Predictions - %div.col-md-2 - %a.btn.btn-info{:href=> to("/faq"), :rel => "external"} - FAQ + /%div.col-md-2 + / %a.btn.btn-info{:href=> to("/faq"), :rel => "external"} + / FAQ %div.container-fluid :javascript -- cgit v1.2.3 From b8d1ce9a588534e1a92bd4461c94b97b6269291c Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 21 Apr 2016 08:18:51 +0000 Subject: removed brackets --- views/prediction.haml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/views/prediction.haml b/views/prediction.haml index 5265504..d8312bb 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -50,13 +50,13 @@ = (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 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."}} + %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", 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 - if type == "Regression" %b 95% Prediction interval: - - interval = prediction[:prediction_interval].nil? ? "[ - - ]" : prediction[:prediction_interval].collect{|i| i.round(2)} + - 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])}] (mg/L)" + = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} (mg/L)" / 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."}} - else -- cgit v1.2.3 From 1a09ee962a769dfe2ef49dcd6fb865381c221788 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 21 Apr 2016 10:29:52 +0000 Subject: updated prediction info --- views/prediction.haml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/views/prediction.haml b/views/prediction.haml index d8312bb..709e17e 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -50,7 +50,7 @@ = (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 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."}} + %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 - if type == "Regression" %b 95% Prediction interval: -- cgit v1.2.3 From b3fffd49c61745e953415c50084fee900d8029e9 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 21 Apr 2016 13:45:20 +0000 Subject: fixed neighbors table; bg-color predictions due to safari; disabled neighbors sort option; enabled table header info icons --- public/images/IST_logo_s.png | Bin 0 -> 7456 bytes views/layout.haml | 17 +++++++++-------- views/neighbors.haml | 24 ++++++++---------------- views/prediction.haml | 10 +++++----- views/style.scss | 4 ++++ 5 files changed, 26 insertions(+), 29 deletions(-) create mode 100644 public/images/IST_logo_s.png diff --git a/public/images/IST_logo_s.png b/public/images/IST_logo_s.png new file mode 100644 index 0000000..eff71af Binary files /dev/null and b/public/images/IST_logo_s.png differ diff --git a/views/layout.haml b/views/layout.haml index a49238f..1220cf5 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -4,7 +4,7 @@ %meta{'charset'=>"utf-8"} %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"} %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"} - %title Lazar Toxicity Predictions + %title lazar Toxicity Predictions %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'} %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"} %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"} @@ -20,17 +20,18 @@ %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 + %header.page-header{:style=>"margin:20px 0 20px;text-align:justify;display:inline-block;width:100%;"} %div.row %div.col-md-2 %a{:href=> to("/predict")} - %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"} + %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"150px", :heigth=>"150px", :style=>"margin:0 3em 0 2em;"} %div.col-md-8 - %h1.media-heading{:style=>"margin: 0 0 0 1em;"} Lazar Toxicity Predictions - /%div.col-md-2 - / %a.btn.btn-info{:href=> to("/faq"), :rel => "external"} - / FAQ - + %h1.media-heading{:style=>"margin: 0 0 0 2em;"} + lazar Toxicity Predictions + %div.col-md-2 + %h1.media-heading{:style=>"margin: 0 0 0 1em;"} + %small + %a{:href=>"https://nano-lazar.in-silico.ch/predict"} nano-lazar %div.container-fluid :javascript $(document).ready(function(){ diff --git a/views/neighbors.haml b/views/neighbors.haml index 2edc3ab..096e432 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -38,7 +38,7 @@ $("table##{j+1}").tablesorter({ debug: false, theme: "bootstrap", - headerTemplate: '{content} {icon}', + headerTemplate: '', widgets: ['columns', 'uitheme', 'stickyHeaders'], widgetOptions: { stickyHeaders_attachTo : '.tab-content', @@ -53,34 +53,26 @@ stickyHeaders_yScroll : null, stickyHeaders_filteredToTop: true }, - headers: {0: {sorter: false}, 3: {sorter: false}}, sortList: [[2,1]], + headers: {sorter: false}, widthFixed: false }); }); - if prediction[:neighbors].size > 0 %div.table-responsive - %table.tablesorter{:id=>"#{j+1}", :style=>"border-style: solid;"} + %table{:id=>"#{j+1}", :style=>"border-style: solid;"} %thead %tr - %th{:style =>"vertical-align:middle;"} + %th.sorter-false{:style =>"vertical-align:middle;"} Compound - %th{:style =>"vertical-align:middle;"} + %th.sorter-false{:style =>"vertical-align:middle;"} Measured Activity - %th{:style =>"vertical-align:middle;"} + %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"} + %th.sorter-false{:style =>"vertical-align:middle;"} Similarity + %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Tanimoto/Jaccard similarity based on Molprint2D fingerprints."}, :style=>"z-index:auto+10;"} / %th{:style =>"vertical-align:middle;"} / Supporting Information - %span - %tr - %td - %td{:style=>"font-size:x-small;padding:0px;"} - / 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;"} - %td{:style=>"font-size:x-small;padding:0px;"} - / 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;"} - / %td %tbody - type = @model_types[j] - unit = @models[j].unit diff --git a/views/prediction.haml b/views/prediction.haml index 709e17e..0f3d57b 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -12,7 +12,7 @@ / displays all prediction result in first table %h3 Prediction Results: %div.table-responsive - %table.table.table-bordered{:id=>"overview", :style=>"background-color:white;"} + %table.table.table-bordered{:id=>"overview"} %tbody %tr %td{:id=>"compound", :style=>"vertical-align:top;"} @@ -35,9 +35,9 @@ %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); '%.2e' % v + " (#{unit})"+"|#{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(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 + " (#{unit})"+", #{'%.2e' % weight} #{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") ? "#{"%.2e" % prediction[:value]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] %p %b Compound is part of the training dataset - elsif prediction[:neighbors].size > 0 @@ -50,13 +50,13 @@ = (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."}} + %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 - 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])} (mg/L)" + = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" / prediction intervall popover %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}} - else diff --git a/views/style.scss b/views/style.scss index 70c8035..29f532b 100644 --- a/views/style.scss +++ b/views/style.scss @@ -37,3 +37,7 @@ img { .faq h1 { text-align: center; } +.tablesorter-bootstrap thead .sorter-false { + cursor: default; +} + -- cgit v1.2.3 From feb1a1cef0d750d009e72914345dc4bf2bd625ba Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 25 Apr 2016 16:01:07 +0000 Subject: added links;share;acknowledgements --- public/images/Google+.png | Bin 0 -> 432 bytes public/images/LinkedIn.png | Bin 0 -> 356 bytes public/images/Twitter.png | Bin 0 -> 379 bytes public/images/bfr_logo.gif | Bin 0 -> 6605 bytes public/images/enm_logo.png | Bin 0 -> 47307 bytes public/images/ot_logo.png | Bin 0 -> 27320 bytes views/layout.haml | 53 ++++++++++++++++++++++++++++++++++++++++----- views/style.scss | 27 ++++++++++++++++++++++- 8 files changed, 73 insertions(+), 7 deletions(-) create mode 100644 public/images/Google+.png create mode 100644 public/images/LinkedIn.png create mode 100644 public/images/Twitter.png create mode 100644 public/images/bfr_logo.gif create mode 100644 public/images/enm_logo.png create mode 100644 public/images/ot_logo.png diff --git a/public/images/Google+.png b/public/images/Google+.png new file mode 100644 index 0000000..9db76fd Binary files /dev/null and b/public/images/Google+.png differ diff --git a/public/images/LinkedIn.png b/public/images/LinkedIn.png new file mode 100644 index 0000000..dcdda37 Binary files /dev/null and b/public/images/LinkedIn.png differ diff --git a/public/images/Twitter.png b/public/images/Twitter.png new file mode 100644 index 0000000..05e0c2c Binary files /dev/null and b/public/images/Twitter.png differ diff --git a/public/images/bfr_logo.gif b/public/images/bfr_logo.gif new file mode 100644 index 0000000..1d6d36b Binary files /dev/null and b/public/images/bfr_logo.gif differ diff --git a/public/images/enm_logo.png b/public/images/enm_logo.png new file mode 100644 index 0000000..cac2dd3 Binary files /dev/null and b/public/images/enm_logo.png differ diff --git a/public/images/ot_logo.png b/public/images/ot_logo.png new file mode 100644 index 0000000..7dfa6f9 Binary files /dev/null and b/public/images/ot_logo.png differ diff --git a/views/layout.haml b/views/layout.haml index 1220cf5..09968e9 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -20,7 +20,7 @@ %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{:style=>"margin:20px 0 20px;text-align:justify;display:inline-block;width:100%;"} + %header.page-header %div.row %div.col-md-2 %a{:href=> to("/predict")} @@ -29,10 +29,14 @@ %h1.media-heading{:style=>"margin: 0 0 0 2em;"} lazar Toxicity Predictions %div.col-md-2 - %h1.media-heading{:style=>"margin: 0 0 0 1em;"} + %h1.media-heading %small - %a{:href=>"https://nano-lazar.in-silico.ch/predict"} nano-lazar + %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar + %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old version + %div.container-fluid + Problems, bugs, ideas for improvements ? Please report at our + %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker :javascript $(document).ready(function(){ $("#back-top").hide(); @@ -40,14 +44,51 @@ $(this).attr('src', '/images/blind.png'); }); }); + $(document).ready(function(){ + $('[data-toggle="popover"]').popover(); + $('.modal').on('hidden.bs.modal', function () { + $(this).removeData('bs.modal'); + }); + }); = yield %footer.footer %div.container-fluid - %p.text-muted - © - %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology gmbh 2004 - #{Time.now.year.to_s} + %div.row + %div.col-md-8 + %p.text-muted + © + %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology gmbh 2004 - #{Time.now.year.to_s} + %div.col-md-4 + %button.btn.btn-default{:type=>"button", :data=>{:toggle=>"modal", :target=>"#acknowledgements"}} acknowledgements + %div.modal.fade{:id=>"acknowledgements", :role=>"dialog"} + %div.modal-dialog + %div.modal-content + %div.modal-header + %button{:type=>"button", :class=>"close", :data=>{:dismiss=>"modal"}} + × + %h4.modal-title Financial support: + %div.modal-body + %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"} + %img{:src=>"/images/bfr_logo.gif"} + %a{:href=>"http://www.opentox.org/", :target=>"_blank"} + %img{:src=>"/images/ot_logo.png"} + %a{:href=>"https://enanomapper.net/", :target=>"_blank"} + %img{:src=>"/images/enm_logo.png"} + + %div.btn-group.dropup + %button.btn.btn-default.dropdown-toggle{:data=>{:toggle=>"dropdown"}, :aria=>{:haspopup=>"true", :expanded=>"false"}} share + %ul.dropdown-menu{:class=>"share-buttons"} + %li + %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{:src=>"/images/Twitter.png"} + %li + %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"} + %img{:src=>"/images/Google+.png"} + %li + %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{:src=>"/images/LinkedIn.png"} #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"} %a{:href => "", :style=>"text:decoration:none;color:#ccc;"} diff --git a/views/style.scss b/views/style.scss index 29f532b..77c7c4e 100644 --- a/views/style.scss +++ b/views/style.scss @@ -40,4 +40,29 @@ img { .tablesorter-bootstrap thead .sorter-false { cursor: default; } - +ul.share-buttons{ + list-style: none; +} +.dropdown-menu { + min-width: 0px !important; + width:60px; +} +.dropdown-menu a { + padding: 0 2px 1px 2px !important; +} +.page-header{ + margin:20px 0 20px; + text-align:justify; + display:inline-block; + width:98.5%; +} +.footer .modal img{ + width: 250px; + padding: 1em; +} +footer button{ + padding-bottom: 1em !important; +} +.dropdown-menu img{ + margin-left: 0.7em; +} -- cgit v1.2.3 From 6c330fdcdf4ac941b0dab1aeb1add75bb5c4eae2 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 25 Apr 2016 16:09:59 +0000 Subject: added content to acknowledgement --- public/images/nestec.jpg | Bin 0 -> 14209 bytes views/layout.haml | 2 ++ 2 files changed, 2 insertions(+) create mode 100644 public/images/nestec.jpg diff --git a/public/images/nestec.jpg b/public/images/nestec.jpg new file mode 100644 index 0000000..ba1c335 Binary files /dev/null and b/public/images/nestec.jpg differ diff --git a/views/layout.haml b/views/layout.haml index 09968e9..5965ee1 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -76,6 +76,8 @@ %img{:src=>"/images/ot_logo.png"} %a{:href=>"https://enanomapper.net/", :target=>"_blank"} %img{:src=>"/images/enm_logo.png"} + %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"} + %img{:src=>"/images/nestec.jpg"} %div.btn-group.dropup %button.btn.btn-default.dropdown-toggle{:data=>{:toggle=>"dropdown"}, :aria=>{:haspopup=>"true", :expanded=>"false"}} share -- cgit v1.2.3 From 02357098113713b5ac5268ac19bf9443804c930e Mon Sep 17 00:00:00 2001 From: gebele Date: Fri, 29 Apr 2016 06:58:00 +0000 Subject: changed share and acknowledgement always visible --- public/images/Facebook.png | Bin 0 -> 318 bytes views/layout.haml | 59 +++++++++++++++++++-------------------------- views/style.scss | 18 ++++++++------ 3 files changed, 35 insertions(+), 42 deletions(-) create mode 100755 public/images/Facebook.png diff --git a/public/images/Facebook.png b/public/images/Facebook.png new file mode 100755 index 0000000..3d249fd Binary files /dev/null and b/public/images/Facebook.png differ diff --git a/views/layout.haml b/views/layout.haml index 5965ee1..43e1233 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -32,11 +32,22 @@ %h1.media-heading %small %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar - %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old version %div.container-fluid - Problems, bugs, ideas for improvements ? Please report at our - %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker + %topline + Problems, bugs, ideas for improvements ? Please report at our + %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker. + | + %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old version + | + %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"} :javascript $(document).ready(function(){ $("#back-top").hide(); @@ -56,41 +67,21 @@ %footer.footer %div.container-fluid %div.row - %div.col-md-8 + %div.col-md-12 %p.text-muted © %a{:href => 'http://www.in-silico.ch', :rel => "external"} in silico toxicology gmbh 2004 - #{Time.now.year.to_s} - %div.col-md-4 - %button.btn.btn-default{:type=>"button", :data=>{:toggle=>"modal", :target=>"#acknowledgements"}} acknowledgements - %div.modal.fade{:id=>"acknowledgements", :role=>"dialog"} - %div.modal-dialog - %div.modal-content - %div.modal-header - %button{:type=>"button", :class=>"close", :data=>{:dismiss=>"modal"}} - × - %h4.modal-title Financial support: - %div.modal-body - %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"} - %img{:src=>"/images/bfr_logo.gif"} - %a{:href=>"http://www.opentox.org/", :target=>"_blank"} - %img{:src=>"/images/ot_logo.png"} - %a{:href=>"https://enanomapper.net/", :target=>"_blank"} - %img{:src=>"/images/enm_logo.png"} - %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"} - %img{:src=>"/images/nestec.jpg"} + %supporters.col-md-12 + %p Financial support: + %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"} + %img{:src=>"/images/bfr_logo.gif"} + %a{:href=>"http://www.opentox.org/", :target=>"_blank"} + %img{:src=>"/images/ot_logo.png"} + %a{:href=>"https://enanomapper.net/", :target=>"_blank"} + %img{:src=>"/images/enm_logo.png"} + %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"} + %img{:src=>"/images/nestec.jpg"} - %div.btn-group.dropup - %button.btn.btn-default.dropdown-toggle{:data=>{:toggle=>"dropdown"}, :aria=>{:haspopup=>"true", :expanded=>"false"}} share - %ul.dropdown-menu{:class=>"share-buttons"} - %li - %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{:src=>"/images/Twitter.png"} - %li - %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"} - %img{:src=>"/images/Google+.png"} - %li - %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{:src=>"/images/LinkedIn.png"} #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"} %a{:href => "", :style=>"text:decoration:none;color:#ccc;"} diff --git a/views/style.scss b/views/style.scss index 77c7c4e..49e03ab 100644 --- a/views/style.scss +++ b/views/style.scss @@ -56,13 +56,15 @@ ul.share-buttons{ display:inline-block; width:98.5%; } -.footer .modal img{ - width: 250px; - padding: 1em; +.share{ + width: 30px; + padding-right: 5px; } -footer button{ - padding-bottom: 1em !important; -} -.dropdown-menu img{ - margin-left: 0.7em; +supporters{ + background-color: white; + + img{ + width: 200px; + margin-right: 1em; + } } -- cgit v1.2.3 From 45dcce0598ec31389991c9e67be2683a8dfcc354 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 3 May 2016 08:44:30 +0000 Subject: final header adjustments --- public/images/Email.png | Bin 0 -> 396 bytes views/layout.haml | 35 +++++++++++++++++++++-------------- 2 files changed, 21 insertions(+), 14 deletions(-) create mode 100755 public/images/Email.png diff --git a/public/images/Email.png b/public/images/Email.png new file mode 100755 index 0000000..1e5c8bf Binary files /dev/null and b/public/images/Email.png differ diff --git a/views/layout.haml b/views/layout.haml index 43e1233..13f351c 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -27,7 +27,7 @@ %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;"} - lazar Toxicity Predictions + lazar toxicity predictions %div.col-md-2 %h1.media-heading %small @@ -35,19 +35,26 @@ %div.container-fluid %topline - Problems, bugs, ideas for improvements ? Please report at our - %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker. - | - %a{:href=>"http://lazar-old.in-silico.ch"} lazar-old version - | - %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 + %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"} + %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"} lazar-old :javascript $(document).ready(function(){ $("#back-top").hide(); -- cgit v1.2.3 From e3eb9ac32762a5b9f58ecfd6aa71419803e77a67 Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 10 May 2016 14:14:20 +0000 Subject: bunped version to 0.9.3 --- Gemfile | 2 +- VERSION | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile b/Gemfile index 8517fde..fbd485e 100644 --- a/Gemfile +++ b/Gemfile @@ -3,4 +3,4 @@ gemspec gem "sinatra" gem "haml" gem "sass" -gem "lazar"#, :path => "../lazar" +gem "lazar" diff --git a/VERSION b/VERSION index 6e8bf73..965065d 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.1.0 +0.9.3 -- cgit v1.2.3 From b86b70e49e54ac21b5fc2451b68f748b2b3a3b7d Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 11 May 2016 08:22:04 +0000 Subject: added bin --- bin/lazar | 3 +++ lazar-gui.gemspec | 16 +++++++--------- 2 files changed, 10 insertions(+), 9 deletions(-) create mode 100755 bin/lazar diff --git a/bin/lazar b/bin/lazar new file mode 100755 index 0000000..f1e82e1 --- /dev/null +++ b/bin/lazar @@ -0,0 +1,3 @@ +#!/bin/bash +`sudo /usr/bin/mongod &` +`unicorn -p 8088 -E production &` diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index db29827..48c3279 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -8,17 +8,15 @@ Gem::Specification.new do |s| s.homepage = "http://github.com/opentox/lazar-gui" s.summary = %q{lazar-gui} s.description = %q{Graphical User Interface for Lazar Toxicology Predictions} - s.license = 'GPL-3' - + s.license = 'GPL-3.0' + s.executables = 'lazar' s.rubyforge_project = "lazar-gui" - s.files = `git ls-files`.split("\n") - s.required_ruby_version = '>= 1.9.2' s.add_runtime_dependency "lazar", "~> 0.9.3" - 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.add_runtime_dependency "sinatra", "~> 1.4.0" + s.add_runtime_dependency "rdiscount", "~> 2.1.0" + s.add_runtime_dependency "haml", "~> 4.0.0" + s.add_runtime_dependency "sass", "~> 3.4.0" + s.add_runtime_dependency "unicorn", "~> 5.1.0" end -- cgit v1.2.3 From b527875be3209966fc4a62a27854b16ed7ba5afd Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 11 May 2016 08:31:01 +0000 Subject: bumped version --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 965065d..a602fc9 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.9.3 +0.9.4 -- cgit v1.2.3 From b0104928c6b8d92c8980dcf42c6c32450fc63c1b Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 11 May 2016 09:40:23 +0000 Subject: added lazar.sh --- VERSION | 2 +- bin/lazar | 8 +++++--- bin/lazar.sh | 3 +++ lazar-gui.gemspec | 2 +- 4 files changed, 10 insertions(+), 5 deletions(-) mode change 100755 => 100644 bin/lazar create mode 100755 bin/lazar.sh diff --git a/VERSION b/VERSION index a602fc9..b0bb878 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.9.4 +0.9.5 diff --git a/bin/lazar b/bin/lazar old mode 100755 new mode 100644 index f1e82e1..0fd2895 --- a/bin/lazar +++ b/bin/lazar @@ -1,3 +1,5 @@ -#!/bin/bash -`sudo /usr/bin/mongod &` -`unicorn -p 8088 -E production &` +#!/usr/bin/env ruby +bin_dir = File.expand_path(File.dirname(__FILE__)) +shell_script_path = File.join(bin_dir, 'lazar.sh') + +`#{shell_script_path}` diff --git a/bin/lazar.sh b/bin/lazar.sh new file mode 100755 index 0000000..28d70a7 --- /dev/null +++ b/bin/lazar.sh @@ -0,0 +1,3 @@ +#!/bin/bash +sudo /usr/bin/mongod & +unicorn -p 8088 -E production & diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index 48c3279..0f61cb2 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -9,7 +9,7 @@ Gem::Specification.new do |s| s.summary = %q{lazar-gui} s.description = %q{Graphical User Interface for Lazar Toxicology Predictions} s.license = 'GPL-3.0' - s.executables = 'lazar' + s.executables = "lazar" s.rubyforge_project = "lazar-gui" s.files = `git ls-files`.split("\n") -- cgit v1.2.3 From 171d6e675a0e1c209340d2988e3a39d06999d18c Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 12 May 2016 10:21:50 +0000 Subject: added start and stop script --- Gemfile | 2 +- application.rb | 4 ++-- bin/lazar | 5 ----- bin/lazar-start | 5 +++++ bin/lazar-start.sh | 20 ++++++++++++++++++++ bin/lazar-stop | 6 ++++++ bin/lazar-stop.sh | 24 ++++++++++++++++++++++++ bin/lazar.sh | 3 --- lazar-gui.gemspec | 6 +++++- 9 files changed, 63 insertions(+), 12 deletions(-) delete mode 100644 bin/lazar create mode 100755 bin/lazar-start create mode 100755 bin/lazar-start.sh create mode 100755 bin/lazar-stop create mode 100755 bin/lazar-stop.sh delete mode 100755 bin/lazar.sh diff --git a/Gemfile b/Gemfile index fbd485e..775c2c4 100644 --- a/Gemfile +++ b/Gemfile @@ -1,6 +1,6 @@ source "https://rubygems.org" gemspec +gem "lazar" gem "sinatra" gem "haml" gem "sass" -gem "lazar" diff --git a/application.rb b/application.rb index 7b774bc..1fa0663 100644 --- a/application.rb +++ b/application.rb @@ -1,5 +1,5 @@ -require_relative 'helper.rb' -require 'rdiscount' +#require_relative 'helper.rb' +#require 'rdiscount' include OpenTox #require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb") # until added to ot-tools diff --git a/bin/lazar b/bin/lazar deleted file mode 100644 index 0fd2895..0000000 --- a/bin/lazar +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env ruby -bin_dir = File.expand_path(File.dirname(__FILE__)) -shell_script_path = File.join(bin_dir, 'lazar.sh') - -`#{shell_script_path}` diff --git a/bin/lazar-start b/bin/lazar-start new file mode 100755 index 0000000..713acf2 --- /dev/null +++ b/bin/lazar-start @@ -0,0 +1,5 @@ +#!/usr/bin/env ruby +bin_dir = File.expand_path(File.dirname(__FILE__)) +shell_script_path = File.join(bin_dir, 'lazar-start.sh') + +`#{shell_script_path}` diff --git a/bin/lazar-start.sh b/bin/lazar-start.sh new file mode 100755 index 0000000..b1ea61c --- /dev/null +++ b/bin/lazar-start.sh @@ -0,0 +1,20 @@ +#!/bin/bash +#R CMD Rserve +#sudo mongod +#unicorn -p 8088 -E production + +RETVAL=0 + +start() { + grep_mongo=`ps aux | grep -v grep | grep mongod` + if [ ${#grep_mongo} -gt 0 ] + then + echo "MongoDB is already running." + else + echo "Start MongoDB." + `sudo mongod` + RETVAL=$? + fi +} + +exit $RETVAL diff --git a/bin/lazar-stop b/bin/lazar-stop new file mode 100755 index 0000000..67e72e9 --- /dev/null +++ b/bin/lazar-stop @@ -0,0 +1,6 @@ +#!/usr/bin/env ruby +bin_dir = File.expand_path(File.dirname(__FILE__)) +shell_script_path = File.join(bin_dir, 'lazar-stop.sh') + +`#{shell_script_path}` + diff --git a/bin/lazar-stop.sh b/bin/lazar-stop.sh new file mode 100755 index 0000000..26de413 --- /dev/null +++ b/bin/lazar-stop.sh @@ -0,0 +1,24 @@ +#!/bin/bash +#R CMD Rserve +#sudo mongod +#unicorn -p 8088 -E production + +RETVAL=0 + +stop() { + grep_mongo=`ps aux | grep -v grep | grep mongod` + if [ ${#grep_mongo} -gt 0 ] + then + echo "Stop MongoDB." + PID=`ps ax | grep -v grep | grep mongod | awk '{ print $1 }'` + for i in "${PID}" + do + `sudo kill -2 $i` + done + RETVAL=$? + else + echo "MongoDB is not running." + fi +} + +exit $RETVAL diff --git a/bin/lazar.sh b/bin/lazar.sh deleted file mode 100755 index 28d70a7..0000000 --- a/bin/lazar.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -sudo /usr/bin/mongod & -unicorn -p 8088 -E production & diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index 0f61cb2..9eec5f4 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -15,8 +15,12 @@ Gem::Specification.new do |s| s.add_runtime_dependency "lazar", "~> 0.9.3" s.add_runtime_dependency "sinatra", "~> 1.4.0" - s.add_runtime_dependency "rdiscount", "~> 2.1.0" + s.add_runtime_dependency "rdiscount", "~> 2.1.0" s.add_runtime_dependency "haml", "~> 4.0.0" s.add_runtime_dependency "sass", "~> 3.4.0" s.add_runtime_dependency "unicorn", "~> 5.1.0" + + s.post_install_message = %q{ + To run the service execute `lazar &`. + } end -- cgit v1.2.3 From 80cdde4c5cd03829518772e71b0bee4133afe622 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 12 May 2016 15:35:03 +0000 Subject: bumped version --- VERSION | 2 +- bin/lazar-start.sh | 23 +++++------------------ bin/lazar-stop.sh | 55 ++++++++++++++++++++++++++++++++++-------------------- lazar-gui.gemspec | 6 ++++-- unicorn.rb | 5 +++++ 5 files changed, 50 insertions(+), 41 deletions(-) diff --git a/VERSION b/VERSION index b0bb878..85b7c69 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.9.5 +0.9.6 diff --git a/bin/lazar-start.sh b/bin/lazar-start.sh index b1ea61c..72facbb 100755 --- a/bin/lazar-start.sh +++ b/bin/lazar-start.sh @@ -1,20 +1,7 @@ #!/bin/bash -#R CMD Rserve -#sudo mongod -#unicorn -p 8088 -E production +lazar-stop +sudo mongod & +R CMD Rserve +unicorn -c unicorn.rb -E production -D -RETVAL=0 - -start() { - grep_mongo=`ps aux | grep -v grep | grep mongod` - if [ ${#grep_mongo} -gt 0 ] - then - echo "MongoDB is already running." - else - echo "Start MongoDB." - `sudo mongod` - RETVAL=$? - fi -} - -exit $RETVAL +exit 0 diff --git a/bin/lazar-stop.sh b/bin/lazar-stop.sh index 26de413..f5ba963 100755 --- a/bin/lazar-stop.sh +++ b/bin/lazar-stop.sh @@ -1,24 +1,39 @@ #!/bin/bash -#R CMD Rserve -#sudo mongod -#unicorn -p 8088 -E production +grep_mongo=`ps aux | grep -v grep | grep mongod` +grep_rserve=`ps aux | grep -v grep | grep Rserve` +grep_unicorn=`ps aux | grep -v grep | grep unicorn` -RETVAL=0 +# mongod +if [ ${#grep_mongo} -gt 0 ] +then + PID=`ps ax | grep -v grep | grep mongod | awk '{ print $1 }'` + for i in "${PID}" + do + `sudo kill $i` + done +else + echo "MongoDB is not running." +fi -stop() { - grep_mongo=`ps aux | grep -v grep | grep mongod` - if [ ${#grep_mongo} -gt 0 ] - then - echo "Stop MongoDB." - PID=`ps ax | grep -v grep | grep mongod | awk '{ print $1 }'` - for i in "${PID}" - do - `sudo kill -2 $i` - done - RETVAL=$? - else - echo "MongoDB is not running." - fi -} +# rserve +if [ ${#grep_rserve} -gt 0 ] +then + PID=`ps ax | grep -v grep | grep Rserve | awk '{ print $1 }'` + for i in "${PID}" + do + `kill $i` + done +else + echo "Rserve is not running." +fi -exit $RETVAL +# unicorn +if [ ${#grep_unicorn} -gt 0 ] +then + PID=`ps ax | grep -v grep | grep unicorn | awk '{ print $1 }'` + `kill ${PID[0]}` +else + echo "Unicorn is not running." +fi + +exit 0 diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index 9eec5f4..6c83511 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -9,7 +9,7 @@ Gem::Specification.new do |s| s.summary = %q{lazar-gui} s.description = %q{Graphical User Interface for Lazar Toxicology Predictions} s.license = 'GPL-3.0' - s.executables = "lazar" + s.executables = ["lazar-start", "lazar-stop"] s.rubyforge_project = "lazar-gui" s.files = `git ls-files`.split("\n") @@ -21,6 +21,8 @@ Gem::Specification.new do |s| s.add_runtime_dependency "unicorn", "~> 5.1.0" s.post_install_message = %q{ - To run the service execute `lazar &`. + Service cmds: + lazar-start & + lazar-stop } end diff --git a/unicorn.rb b/unicorn.rb index 7f8d4a2..010ebbb 100644 --- a/unicorn.rb +++ b/unicorn.rb @@ -1,2 +1,7 @@ #worker_processes 4 timeout 6000 +listen 8088 +log_dir = "#{ENV['HOME']}" +log_file = File.join log_dir, "lazar.log" +stderr_path log_file +stdout_path log_file -- cgit v1.2.3 From c8e890d4194a55328c078a2ca7c3b8f534546b43 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 6 Jun 2016 13:53:01 +0000 Subject: bumped version;include unicorn config --- VERSION | 2 +- bin/lazar-start | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 85b7c69..c81aa44 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.9.6 +0.9.7 diff --git a/bin/lazar-start b/bin/lazar-start index 713acf2..b284b8d 100755 --- a/bin/lazar-start +++ b/bin/lazar-start @@ -1,5 +1,7 @@ #!/usr/bin/env ruby bin_dir = File.expand_path(File.dirname(__FILE__)) shell_script_path = File.join(bin_dir, 'lazar-start.sh') +unicorn_config_path = File.join('unicorn.rb') `#{shell_script_path}` +`#{unicorn_config_path}` -- cgit v1.2.3 From 242d18cb8bcfbe3c38cfa38c6b380fda19584d81 Mon Sep 17 00:00:00 2001 From: gebele Date: Mon, 6 Jun 2016 14:42:48 +0000 Subject: undo unicorn config path --- VERSION | 2 +- bin/lazar-start | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/VERSION b/VERSION index c81aa44..e3e1807 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.9.7 +0.9.8 diff --git a/bin/lazar-start b/bin/lazar-start index b284b8d..713acf2 100755 --- a/bin/lazar-start +++ b/bin/lazar-start @@ -1,7 +1,5 @@ #!/usr/bin/env ruby bin_dir = File.expand_path(File.dirname(__FILE__)) shell_script_path = File.join(bin_dir, 'lazar-start.sh') -unicorn_config_path = File.join('unicorn.rb') `#{shell_script_path}` -`#{unicorn_config_path}` -- cgit v1.2.3 From cdd98748e21bf30c5301f37cdec1af8fc9255d7a Mon Sep 17 00:00:00 2001 From: gebele Date: Tue, 7 Jun 2016 09:55:50 +0000 Subject: bumped version; required unicorn conf --- VERSION | 2 +- bin/lazar-start | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/VERSION b/VERSION index e3e1807..7e310ba 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.9.8 +0.9.9 diff --git a/bin/lazar-start b/bin/lazar-start index 713acf2..73f6d91 100755 --- a/bin/lazar-start +++ b/bin/lazar-start @@ -1,5 +1,8 @@ #!/usr/bin/env ruby bin_dir = File.expand_path(File.dirname(__FILE__)) shell_script_path = File.join(bin_dir, 'lazar-start.sh') +app_dir = File.expand_path('..') +unicorn_conf = File.join(app_dir, 'unicorn.rb') `#{shell_script_path}` +`#{unicorn_conf}` -- cgit v1.2.3 From c122a9d758bf96173f60fde0dbc2ae2b5b34b418 Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 8 Jun 2016 06:46:46 +0000 Subject: fixed load path with unicorn --- Gemfile | 1 + VERSION | 2 +- bin/lazar-start.sh | 3 ++- bin/lazar-stop.sh | 13 +++++++++++++ lazar-gui.gemspec | 13 +++++++------ 5 files changed, 24 insertions(+), 8 deletions(-) diff --git a/Gemfile b/Gemfile index 775c2c4..7bade23 100644 --- a/Gemfile +++ b/Gemfile @@ -1,6 +1,7 @@ source "https://rubygems.org" gemspec gem "lazar" +gem "gem-path" gem "sinatra" gem "haml" gem "sass" diff --git a/VERSION b/VERSION index e3e1807..3eefcb9 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -0.9.8 +1.0.0 diff --git a/bin/lazar-start.sh b/bin/lazar-start.sh index 72facbb..9072150 100755 --- a/bin/lazar-start.sh +++ b/bin/lazar-start.sh @@ -1,7 +1,8 @@ #!/bin/bash -lazar-stop sudo mongod & R CMD Rserve +LAZARPATH=$(gem path lazar-gui) +cd $LAZARPATH unicorn -c unicorn.rb -E production -D exit 0 diff --git a/bin/lazar-stop.sh b/bin/lazar-stop.sh index f5ba963..eea6815 100755 --- a/bin/lazar-stop.sh +++ b/bin/lazar-stop.sh @@ -1,8 +1,21 @@ #!/bin/bash +grep_lazar=`ps aux | grep -v grep | grep lazar-start` grep_mongo=`ps aux | grep -v grep | grep mongod` grep_rserve=`ps aux | grep -v grep | grep Rserve` grep_unicorn=`ps aux | grep -v grep | grep unicorn` +# lazar +if [ ${#grep_lazar} -gt 0 ] +then + PID=`ps ax | grep -v grep | grep lazar-start | awk '{ print $1 }'` + for i in "${PID}" + do + `kill $i` + done +else + echo "Lazar is stopped." +fi + # mongod if [ ${#grep_mongo} -gt 0 ] then diff --git a/lazar-gui.gemspec b/lazar-gui.gemspec index 6c83511..af5f0f9 100644 --- a/lazar-gui.gemspec +++ b/lazar-gui.gemspec @@ -13,12 +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" - s.add_runtime_dependency "sinatra", "~> 1.4.0" - s.add_runtime_dependency "rdiscount", "~> 2.1.0" - s.add_runtime_dependency "haml", "~> 4.0.0" - s.add_runtime_dependency "sass", "~> 3.4.0" - s.add_runtime_dependency "unicorn", "~> 5.1.0" + s.add_runtime_dependency "lazar", "~> 0.9.3", '>= 0.9.3' + s.add_runtime_dependency "gem-path", "~> 0.6.1", '>= 0.6.1' + s.add_runtime_dependency "sinatra", "~> 1.4.0", '>= 1.4.0' + s.add_runtime_dependency "rdiscount", "~> 2.1.0", '>= 2.1.0' + s.add_runtime_dependency "haml", "~> 4.0.0", '>= 4.0.0' + s.add_runtime_dependency "sass", "~> 3.4.0", '>= 3.4.0' + s.add_runtime_dependency "unicorn", "~> 5.1.0", '>= 5.1.0' s.post_install_message = %q{ Service cmds: -- cgit v1.2.3 From 769f704a2b4e2d83256f580317ed8c0b48cc4f45 Mon Sep 17 00:00:00 2001 From: gebele Date: Wed, 8 Jun 2016 13:47:51 +0000 Subject: bumped version; added version to GUI --- VERSION | 2 +- application.rb | 1 + views/layout.haml | 5 +++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/VERSION b/VERSION index 3eefcb9..7dea76e 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -1.0.0 +1.0.1 diff --git a/application.rb b/application.rb index 1fa0663..b9c267c 100644 --- a/application.rb +++ b/application.rb @@ -25,6 +25,7 @@ get '/?' do end get '/predict/?' do + @version = File.read("VERSION").chomp @models = OpenTox::Model::Prediction.all @endpoints = @models.collect{|m| m.endpoint}.sort.uniq @models.count <= 0 ? (haml :info) : (haml :predict) diff --git a/views/layout.haml b/views/layout.haml index 13f351c..a40b68c 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -38,10 +38,11 @@ %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 => '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"} -- 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. 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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.) 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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. 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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