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authorChristoph Helma <helma@in-silico.ch>2011-03-09 14:08:29 +0100
committerChristoph Helma <helma@in-silico.ch>2011-03-09 14:08:29 +0100
commita101b1ff1ba3be2ba64655127f67a17d2872fc7b (patch)
tree96f005d95b63e0928a6a909bb6927537660dda2b
parent5c5d66c2a9487687ba9032da04031ad59ab1de46 (diff)
parentc1964f8418296f14d0f3728b5b55354fb9d982f0 (diff)
Merge branch 'release/v1.0.0'
-rw-r--r--.gitignore2
-rw-r--r--LICENSE674
-rw-r--r--README21
-rw-r--r--application.rb539
-rw-r--r--config.ru4
-rw-r--r--helper.rb48
-rw-r--r--model.rb244
-rw-r--r--parser.rb119
-rw-r--r--public/javascripts/jquery-ui-progressbar.js49
-rw-r--r--[-rwxr-xr-x]public/javascripts/jquery.js291
-rwxr-xr-xpublic/javascripts/toxcreate.js124
-rw-r--r--public/progressbar/images/ui-bg_flat_0_aaaaaa_40x100.pngbin0 -> 2062 bytes
-rw-r--r--public/progressbar/images/ui-bg_glass_95_fef1ec_1x400.pngbin0 -> 119 bytes
-rw-r--r--public/progressbar/images/ui-bg_gloss-wave_16_121212_500x100.pngbin0 -> 478 bytes
-rw-r--r--public/progressbar/images/ui-bg_highlight-hard_15_888888_1x100.pngbin0 -> 214 bytes
-rw-r--r--public/progressbar/images/ui-bg_highlight-hard_55_555555_1x100.pngbin0 -> 115 bytes
-rw-r--r--public/progressbar/images/ui-bg_highlight-soft_35_adadad_1x100.pngbin0 -> 145 bytes
-rw-r--r--public/progressbar/images/ui-bg_highlight-soft_60_dddddd_1x100.pngbin0 -> 106 bytes
-rw-r--r--public/progressbar/images/ui-bg_inset-soft_15_121212_1x100.pngbin0 -> 103 bytes
-rw-r--r--public/progressbar/images/ui-icons_666666_256x240.pngbin0 -> 4369 bytes
-rw-r--r--public/progressbar/images/ui-icons_aaaaaa_256x240.pngbin0 -> 4369 bytes
-rw-r--r--public/progressbar/images/ui-icons_bbbbbb_256x240.pngbin0 -> 5355 bytes
-rw-r--r--public/progressbar/images/ui-icons_c98000_256x240.pngbin0 -> 4369 bytes
-rw-r--r--public/progressbar/images/ui-icons_cccccc_256x240.pngbin0 -> 4369 bytes
-rw-r--r--public/progressbar/images/ui-icons_cd0a0a_256x240.pngbin0 -> 4369 bytes
-rw-r--r--public/progressbar/images/ui-icons_f29a00_256x240.pngbin0 -> 4369 bytes
-rw-r--r--public/progressbar/progressbar.css305
-rw-r--r--views/about.haml4
-rw-r--r--views/classification_validation.haml8
-rw-r--r--views/compound_image.haml2
-rw-r--r--views/create.haml19
-rw-r--r--views/delete.haml25
-rw-r--r--views/features.haml13
-rw-r--r--views/fragment.haml1
-rw-r--r--views/help.haml2
-rw-r--r--views/layout.haml14
-rw-r--r--views/lazar.haml114
-rw-r--r--views/login.haml47
-rw-r--r--views/model.haml98
-rw-r--r--views/model_name.haml12
-rw-r--r--views/model_name_edit.haml14
-rw-r--r--views/model_progress.haml1
-rw-r--r--views/model_status.haml3
-rw-r--r--views/models.haml11
-rw-r--r--views/neighbors.haml15
-rw-r--r--views/neighbors_navigation.haml5
-rw-r--r--views/predict.haml4
-rw-r--r--views/prediction.haml8
-rw-r--r--views/style.sass71
-rw-r--r--views/validation.haml32
50 files changed, 1460 insertions, 1483 deletions
diff --git a/.gitignore b/.gitignore
index de4104c..f138bed 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,5 @@
tmp/*
log/*
TODO
+documentation/
+*.*~
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index 94a9ed0..0000000
--- a/LICENSE
+++ /dev/null
@@ -1,674 +0,0 @@
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- 13. Use with the GNU Affero General Public License.
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- but WITHOUT ANY WARRANTY; without even the implied warranty of
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-Also add information on how to contact you by electronic and paper mail.
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-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
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-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/README b/README
deleted file mode 100644
index 50cc8c3..0000000
--- a/README
+++ /dev/null
@@ -1,21 +0,0 @@
-A graphical interface for the OpenTox ToxModel usecase
-
-INSTALLATION
-
-1. Follow the instructions on http://wiki.github.com/helma/opentox-documentation/installation-of-opentox-webservices
-
-2. Install opentox-toxmodel
-
- git clone git://github.com/helma/opentox-toxmodel.git
-
- or fork opentox-toxmodel on github (http://github.com/helma/opentox-toxmodel) and clone your new repository (see guides on http://github.com)
-
-3. Run opentox-toxmodel
-
- cd opentox-toxmodel
- thin -R config.ru -e production start
-
- point your browser to http://localhost:3000/
-
- or deploy with phusion passenger (http://www.modrails.com/)
-
diff --git a/application.rb b/application.rb
index 9616841..1771661 100644
--- a/application.rb
+++ b/application.rb
@@ -1,259 +1,416 @@
['rubygems', "haml", "sass", "rack-flash"].each do |lib|
- require lib
+ require lib
end
-gem "opentox-ruby-api-wrapper", "= 1.6.5"
-require 'opentox-ruby-api-wrapper'
+gem "opentox-ruby", "~> 1"
+require 'opentox-ruby'
gem 'sinatra-static-assets'
require 'sinatra/static_assets'
require 'ftools'
require File.join(File.dirname(__FILE__),'model.rb')
require File.join(File.dirname(__FILE__),'helper.rb')
-require File.join(File.dirname(__FILE__),'parser.rb')
+use Rack::Session::Cookie, :expire_after => 28800,
+ :secret => "ui6vaiNi-change_me"
use Rack::Flash
-set :sessions, true
+
+set :lock, true
+
+helpers do
+
+ def error(message)
+ LOGGER.error message
+ @model.update :status => "Error", :error_messages => message
+ flash[:notice] = message
+ redirect url_for('/create')
+ end
+
+ private
+ def delete_model(model, subjectid=nil)
+ task = OpenTox::Task.create("Deleting model: #{model.uri}",url_for("/delete",:full)) do |task|
+ begin RestClient.put(File.join(model.task_uri, 'Cancelled'),subjectid) if model.task_uri rescue LOGGER.warn "Cannot cancel task #{model.task_uri}" end
+ task.progress(15)
+ delete_dependent(model.uri, subjectid) if model.uri
+ task.progress(30)
+ delete_dependent(model.validation_uri, subjectid) if model.validation_uri
+ task.progress(45)
+ delete_dependent(model.validation_report_uri, subjectid) if model.validation_report_uri
+ task.progress(60)
+ delete_dependent(model.validation_qmrf_uri, subjectid) if model.validation_qmrf_uri
+ task.progress(75)
+ delete_dependent(model.training_dataset, subjectid) if model.training_dataset
+ task.progress(90)
+ delete_dependent(model.feature_dataset, subjectid) if model.feature_dataset
+ task.progress(100)
+ ""
+ end
+ end
+
+ def delete_dependent(uri, subjectid=nil)
+ begin
+ RestClient.delete(uri, :subjectid => subjectid) if subjectid
+ RestClient.delete(uri) if !subjectid
+ rescue
+ LOGGER.warn "Can not delete uri: #{uri}"
+ end
+ end
+end
+
+before do
+ if !logged_in and !( env['REQUEST_URI'] =~ /\/login$/ and env['REQUEST_METHOD'] == "POST" ) #or !AA_SERVER
+ login("guest","guest")
+ end
+end
get '/?' do
- redirect url_for('/create')
+ redirect url_for('/create')
end
-get '/models/?' do
- @models = ToxCreateModel.all(:order => [ :created_at.desc ])
- @models.each { |model| model.process }
- haml :models
+get '/login' do
+ haml :login
end
-delete '/model/:id/?' do
- model = ToxCreateModel.get(params[:id])
- begin
- RestClient.delete model.uri if model.uri
- RestClient.delete model.task_uri if model.task_uri
- model.destroy!
- flash[:notice] = "#{model.name} model deleted."
- rescue
- flash[:notice] = "#{model.name} model delete error."
- end
- redirect url_for('/models')
+get '/models/?' do
+ @models = ToxCreateModel.all.reverse
+ subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : ""
+ haml :models, :locals=>{:models=>@models, :subjectstring => subjectstring}
end
get '/model/:id/status/?' do
response['Content-Type'] = 'text/plain'
- model = ToxCreateModel.get(params[:id])
- begin
- haml :model_status, :locals=>{:model=>model}, :layout => false
- rescue
+ model = ToxCreateModel.get(params[:id])
+ begin
+ haml :model_status, :locals=>{:model=>model}, :layout => false
+ rescue
+ return "Model #{params[:id]} not available"
+ end
+end
+
+get '/model/:id/progress/?' do
+ response['Content-Type'] = 'text/plain'
+ model = ToxCreateModel.get(params[:id])
+ if model.task_uri
+ if (OpenTox::Task.exist?(model.task_uri))
+ task = OpenTox::Task.exist?(model.task_uri)
+ percentage_completed = task.percentageCompleted
+ end
+ begin
+ haml :model_progress, :locals=>{:percentage_completed=>percentage_completed}, :layout => false
+ rescue
+ return "unavailable"
+ end
+ else
+ return ""
+ end
+end
+
+get '/model/:id/name/?' do
+ response['Content-Type'] = 'text/plain'
+ model = ToxCreateModel.get(params[:id])
+ begin
+ case params[:mode]
+ when 'edit'
+ haml :model_name_edit, :locals=>{:model=>model}, :layout => false
+ when 'show'
+ haml :model_name, :locals=>{:model=>model}, :layout => false
+ else
+ params.inspect
+ end
+ rescue
return "unavailable"
- end
+ end
end
-get '/model/:id/:view/?' do
+put '/model/:id/?' do
response['Content-Type'] = 'text/plain'
- model = ToxCreateModel.get(params[:id])
+ model = ToxCreateModel.get(params[:id])
+ begin
+ model.update :name => params[:name] if params[:name] && model.name != params[:name]
+ redirect url_for("/model/#{model.id}/name?mode=show")
+ rescue
+ return "unavailable"
+ end
+end
+
+get '/model/:id/:view/?' do
+ response['Content-Type'] = 'text/plain'
+ model = ToxCreateModel.get(params[:id])
+ subjectstring = session[:subjectid] ? "?subjectid=#{CGI.escape(session[:subjectid])}" : ""
begin
- model.process
- model.save
case params[:view]
when "model"
- haml :model, :locals=>{:model=>model}, :layout => false
- when /validation/
- haml :validation, :locals=>{:model=>model}, :layout => false
- #if model.type == "classification"
- #haml :classification_validation, :locals=>{:model=>model}, :layout => false
- #elsif model.type == "regression"
- #haml :regression_validation, :locals=>{:model=>model}, :layout => false
- #else
- #return "Unknown model type '#{model.type}'"
- #end
- else
- return "unable to render model: id #{params[:id]}, view #{params[:view]}"
- end
- rescue
+ haml :model, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false
+ when /validation/
+ haml :validation, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false
+ else
+ return "unable to render model: id #{params[:id]}, view #{params[:view]}"
+ end
+ rescue
return "unable to render model: id #{params[:id]}, view #{params[:view]}"
- end
+ end
end
get '/predict/?' do
- @models = ToxCreateModel.all(:order => [ :created_at.desc ])
- @models = @models.collect{|m| m if m.status == 'Completed'}.compact
- haml :predict
+ @models = ToxCreateModel.all.reverse
+ @models = @models.collect{|m| m if m.status == 'Completed'}.compact
+ haml :predict
end
get '/create' do
- haml :create
+ haml :create
end
get '/help' do
- haml :help
+ haml :help
end
get "/confidence" do
- haml :confidence
+ haml :confidence
+end
+
+# proxy to get data from compound service
+# (jQuery load does not work with external URIs)
+get %r{/compound/(.*)} do |inchi|
+ inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'')
+ OpenTox::Compound.from_inchi(inchi).to_names.join(', ')
end
-post '/upload' do # create a new model
-
- if params[:endpoint] == ''
- flash[:notice] = "Please enter an endpoint name."
- redirect url_for('/create')
- end
- unless params[:endpoint] and params[:file] and params[:file][:tempfile]
- flash[:notice] = "Please enter an endpoint name and upload a Excel or CSV file."
- redirect url_for('/create')
- end
-
- @model = ToxCreateModel.new
- @model.name = params[:endpoint]
- feature_uri = url_for("/feature#"+URI.encode(params[:endpoint]), :full)
- parser = Parser.new params[:file], feature_uri
-
- unless parser.format_errors.empty?
- flash[:notice] = "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} formats."
- end
-
- if parser.dataset.compounds.empty?
- flash[:notice] = "Dataset #{params[:file][:filename]} is empty."
- redirect url_for('/create')
- end
-
- begin
- @model.task_uri = OpenTox::Algorithm::Lazar.create_model(:dataset_uri => parser.dataset_uri, :prediction_feature => feature_uri)
- rescue
- flash[:notice] = "Model creation failed. Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format."
- redirect url_for('/create')
- end
+post '/models' do # create a new model
+ unless params[:file] and params[:file][:tempfile] #params[:endpoint] and
+ flash[:notice] = "Please upload a Excel or CSV file."
+ redirect url_for('/create')
+ end
- begin
- validation_task_uri = OpenTox::Validation.crossvalidation(
- :algorithm_uri => OpenTox::Algorithm::Lazar.uri,
- :dataset_uri => parser.dataset_uri,
- :prediction_feature => feature_uri,
- :algorithm_params => "feature_generation_uri=#{OpenTox::Algorithm::Fminer.uri}"
- ).uri
- LOGGER.debug "Validation task: " + validation_task_uri
- @model.validation_task_uri = validation_task_uri
- rescue
- flash[:notice] = "Model validation failed."
+ unless logged_in()
+ logout
+ flash[:notice] = "Please login to create a new model."
+ redirect url_for('/create')
end
+ subjectid = session[:subjectid] ? session[:subjectid] : nil
+ @model = ToxCreateModel.create(:name => params[:file][:filename].sub(/\..*$/,""), :subjectid => subjectid)
+ @model.update :web_uri => url_for("/model/#{@model.id}", :full), :warnings => ""
+ task = OpenTox::Task.create("Uploading dataset and creating lazar model",url_for("/models",:full)) do |task|
-=begin
- if parser.nr_compounds < 10
- flash[:notice] = "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/excel_format"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
- redirect url_for('/create')
- end
-=end
+ task.progress(5)
+ @model.update :status => "Uploading and saving dataset"
+ begin
+ @dataset = OpenTox::Dataset.create(nil, subjectid)
+ # check format by extension - not all browsers provide correct content-type])
+ case File.extname(params[:file][:filename])
+ when ".csv"
+ csv = params[:file][:tempfile].read
+ @dataset.load_csv(csv, subjectid)
+ when ".xls", ".xlsx"
+ @dataset.load_spreadsheet(Excel.new params[:file][:tempfile].path, subjectid)
+ else
+ error "#{params[:file][:filename]} has a unsupported file type."
+ end
+ rescue => e
+ error "Dataset creation failed with #{e.message}"
+ end
+ @dataset.save(subjectid)
+ task.progress(10)
+ if @dataset.compounds.size < 10
+ error "Too few compounds to create a prediction model. Did you provide compounds in SMILES format and classification activities as described in the #{link_to "instructions", "/excel_format"}? As a rule of thumb you will need at least 100 training compounds for nongeneric datasets. A lower number could be sufficient for congeneric datasets."
+ end
+ if @dataset.features.keys.size != 1
+ error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again."
+ end
+ if @dataset.metadata[OT.Errors]
+ error "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} formats."
+ end
+ @model.update :training_dataset => @dataset.uri, :nr_compounds => @dataset.compounds.size, :status => "Creating prediction model"
+ @model.update :warnings => @dataset.metadata[OT.Warnings] unless @dataset.metadata[OT.Warnings].empty?
+ task.progress(15)
+ begin
+ lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :subjectid => subjectid)
+ rescue => e
+ error "Model creation failed with '#{e.message}'. Please check if the input file is in a valid #{link_to "Excel", "/excel_format"} or #{link_to "CSV", "/csv_format"} format."
+ end
+ task.progress(25)
+ type = "unknown"
+ case lazar.metadata[OT.isA]
+ when /Classification/
+ type = "classification"
+ when /Regression/
+ type = "regression"
+ end
+ @model.update :type => type, :feature_dataset => lazar.metadata[OT.featureDataset], :uri => lazar.uri
- @model.nr_compounds = parser.nr_compounds
- @model.warnings = ''
+ unless url_for("",:full).match(/localhost/)
+ @model.update :status => "Validating model"
+ begin
+ validation = OpenTox::Crossvalidation.create(
+ {:algorithm_uri => lazar.metadata[OT.algorithm],
+ :dataset_uri => lazar.parameter("dataset_uri"),
+ :subjectid => subjectid,
+ :prediction_feature => lazar.parameter("prediction_feature"),
+ :algorithm_params => "feature_generation_uri=#{lazar.parameter("feature_generation_uri")}"},
+ nil, OpenTox::SubTask.new(task,25,80))
+ @model.update(:validation_uri => validation.uri)
+ LOGGER.debug "Validation URI: #{@model.validation_uri}"
- @model.warnings += "<p>Incorrect Smiles structures (ignored):</p>" + parser.smiles_errors.join("<br/>") unless parser.smiles_errors.empty?
- @model.warnings += "<p>Irregular activities (ignored):</p>" + parser.activity_errors.join("<br/>") unless parser.activity_errors.empty?
- duplicate_warnings = ''
- parser.duplicates.each {|inchi,lines| duplicate_warnings += "<p>#{lines.join('<br/>')}</p>" if lines.size > 1 }
- @model.warnings += "<p>Duplicated structures (all structures/activities used for model building, please make sure, that the results were obtained from <em>independent</em> experiments):</p>" + duplicate_warnings unless duplicate_warnings.empty?
- @model.save
+ # create summary
+ validation.summary(subjectid).each do |k,v|
+ #LOGGER.debug "mr ::: k: #{k.inspect} - v: #{v.inspect}"
+ begin
+ eval "@model.update :#{k.to_s} => v" if v
+ rescue
+ eval "@model.update :#{k.to_s} => 0"
+ end
+ end
- flash[:notice] = "Model creation and validation started - this may last up to several hours depending on the number and size of the training compounds."
- redirect url_for('/models')
+ @model.update :status => "Creating validation report"
+ validation_report_uri = validation.find_or_create_report(subjectid, OpenTox::SubTask.new(task,80,90)) #unless @model.dirty?
+ @model.update :validation_report_uri => validation_report_uri, :status => "Creating QMRF report"
+ qmrf_report = OpenTox::Crossvalidation::QMRFReport.create(@model.uri, subjectid, OpenTox::SubTask.new(task,90,99))
+ @model.update(:validation_qmrf_uri => qmrf_report.uri, :status => "Completed")
+
+ rescue => e
+ LOGGER.debug "Model validation failed with #{e.message}."
+ @model.save # to avoid dirty models
+ @model.update :warnings => @model.warnings + "\nModel validation failed with #{e.message}.", :status => "Error", :error_messages => e.message
+ end
+
+ end
+
+
+ #@model.warnings += "<p>Incorrect Smiles structures (ignored):</p>" + parser.smiles_errors.join("<br/>") unless parser.smiles_errors.empty?
+ #@model.warnings += "<p>Irregular activities (ignored):</p>" + parser.activity_errors.join("<br/>") unless parser.activity_errors.empty?
+ #duplicate_warnings = ''
+ #parser.duplicates.each {|inchi,lines| duplicate_warnings += "<p>#{lines.join('<br/>')}</p>" if lines.size > 1 }
+ #@model.warnings += "<p>Duplicated structures (all structures/activities used for model building, please make sure, that the results were obtained from <em>independent</em> experiments):</p>" + duplicate_warnings unless duplicate_warnings.empty?
+ lazar.uri
+ end
+ @model.update(:task_uri => task.uri)
+
+ flash[:notice] = "Model creation and validation started - this may last up to several hours depending on the number and size of the training compounds."
+ redirect url_for('/models')
- # TODO: check for empty model
end
post '/predict/?' do # post chemical name to model
- @identifier = params[:identifier]
- unless params[:selection] and params[:identifier] != ''
- flash[:notice] = "Please enter a compound identifier and select an endpoint from the list."
- redirect url_for('/predict')
- end
- begin
- @compound = OpenTox::Compound.new(:name => params[:identifier])
- rescue
- flash[:notice] = "Could not find a structure for '#{@identifier}'. Please try again."
- redirect url_for('/predict')
- end
- @predictions = []
- params[:selection].keys.each do |id|
- model = ToxCreateModel.get(id.to_i)
- model.process unless model.uri
- prediction = nil
- confidence = nil
- title = nil
- db_activities = []
- #LOGGER.debug "curl -X POST -d 'compound_uri=#{@compound.uri}' -H 'Accept:application/x-yaml' #{model.uri}"
- prediction = YAML.load(`curl -X POST -d 'compound_uri=#{@compound.uri}' -H 'Accept:application/x-yaml' #{model.uri}`)
- #prediction = YAML.load(OpenTox::Model::Lazar.predict(params[:compound_uri],params[:model_uri]))
- source = prediction.creator
- if prediction.data[@compound.uri]
- if source.to_s.match(/model/) # real prediction
- prediction = prediction.data[@compound.uri].first.values.first
- #LOGGER.debug prediction[File.join(@@config[:services]["opentox-model"],"lazar#classification")]
- #LOGGER.debug prediction[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]
- if !prediction[File.join(@@config[:services]["opentox-model"],"lazar#classification")].nil?
- @predictions << {
- :title => model.name,
- :model_uri => model.uri,
- :prediction => prediction[File.join(@@config[:services]["opentox-model"],"lazar#classification")],
- :confidence => prediction[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]
- }
- elsif !prediction[File.join(@@config[:services]["opentox-model"],"lazar#regression")].nil?
- @predictions << {
- :title => model.name,
- :model_uri => model.uri,
- :prediction => prediction[File.join(@@config[:services]["opentox-model"],"lazar#regression")],
- :confidence => prediction[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]
- }
- end
- else # database value
- prediction = prediction.data[@compound.uri].first.values
- @predictions << {:title => model.name, :measured_activities => prediction}
- end
- else
- @predictions << {:title => model.name, :prediction => "not available (not enough similar compounds in the training dataset)"}
- end
- end
- LOGGER.debug @predictions.inspect
-
- haml :prediction
+ subjectid = session[:subjectid] ? session[:subjectid] : nil
+ @identifier = params[:identifier]
+ unless params[:selection] and params[:identifier] != ''
+ flash[:notice] = "Please enter a compound identifier and select an endpoint from the list."
+ redirect url_for('/predict')
+ end
+ begin
+ @compound = OpenTox::Compound.from_name(params[:identifier])
+ rescue
+ flash[:notice] = "Could not find a structure for '#{@identifier}'. Please try again."
+ redirect url_for('/predict')
+ end
+ @predictions = []
+ params[:selection].keys.each do |id|
+ model = ToxCreateModel.get(id.to_i)
+ prediction = nil
+ confidence = nil
+ title = nil
+ db_activities = []
+ lazar = OpenTox::Model::Lazar.new model.uri
+ prediction_dataset_uri = lazar.run({:compound_uri => @compound.uri, :subjectid => subjectid})
+ prediction_dataset = OpenTox::LazarPrediction.find(prediction_dataset_uri, subjectid)
+ if prediction_dataset.metadata[OT.hasSource].match(/dataset/)
+ @predictions << {
+ :title => model.name,
+ :measured_activities => prediction_dataset.measured_activities(@compound)
+ }
+ else
+ predicted_feature = prediction_dataset.metadata[OT.dependentVariables]
+ prediction = OpenTox::Feature.find(predicted_feature)
+ if prediction.metadata[OT.error]
+ @predictions << {
+ :title => model.name,
+ :error => prediction.metadata[OT.error]
+ }
+ else
+ @predictions << {
+ :title => model.name,
+ :model_uri => model.uri,
+ :prediction => prediction.metadata[OT.prediction],
+ :confidence => prediction.metadata[OT.confidence]
+ }
+ end
+ end
+ # TODO failed/unavailable predictions
+ end
+
+ haml :prediction
end
post "/lazar/?" do # get detailed prediction
@page = 0
@page = params[:page].to_i if params[:page]
@model_uri = params[:model_uri]
- @prediction = YAML.load(OpenTox::Model::Lazar.predict(params[:compound_uri],params[:model_uri]))
- @compound = OpenTox::Compound.new(:uri => params[:compound_uri])
- @title = @prediction.title
- if @prediction.data[@compound.uri]
- if @prediction.creator.to_s.match(/model/) # real prediction
- p = @prediction.data[@compound.uri].first.values.first
- if !p[File.join(@@config[:services]["opentox-model"],"lazar#classification")].nil?
- feature = File.join(@@config[:services]["opentox-model"],"lazar#classification")
- elsif !p[File.join(@@config[:services]["opentox-model"],"lazar#regression")].nil?
- feature = File.join(@@config[:services]["opentox-model"],"lazar#regression")
- end
- @activity = p[feature]
- @confidence = p[File.join(@@config[:services]["opentox-model"],"lazar#confidence")]
- @neighbors = p[File.join(@@config[:services]["opentox-model"],"lazar#neighbors")]
- @features = p[File.join(@@config[:services]["opentox-model"],"lazar#features")]
- else # database value
- @measured_activities = @prediction.data[@compound.uri].first.values
- end
+ lazar = OpenTox::Model::Lazar.new @model_uri
+ prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => params[:subjectid])
+ @prediction = OpenTox::LazarPrediction.find(prediction_dataset_uri, session[:subjectid])
+ @compound = OpenTox::Compound.new(params[:compound_uri])
+ haml :lazar
+end
+
+post '/login' do
+ if params[:username] == '' || params[:password] == ''
+ flash[:notice] = "Please enter username and password."
+ redirect url_for('/login')
+ end
+ if login(params[:username], params[:password])
+ flash[:notice] = "Welcome #{session[:username]}!"
+ redirect url_for('/create')
else
- @activity = "not available (no similar compounds in the training dataset)"
+ flash[:notice] = "Login failed. Please try again."
+ haml :login
end
- haml :lazar
end
-# proxy to get data from compound service
-# (jQuery load does not work with external URIs)
-get %r{/compound/(.*)} do |inchi|
- OpenTox::Compound.new(:inchi => inchi).names.gsub(/\n/,', ')
+post '/logout' do
+ logout
+ redirect url_for('/login')
+end
+
+delete '/model/:id/?' do
+ model = ToxCreateModel.get(params[:id])
+ raise OpenTox::NotFoundError.new("Model with id: #{params[:id]} not found!") unless model
+ begin
+ delete_model(model, @subjectid)
+ model.delete
+ unless ToxCreateModel.get(params[:id])
+ begin
+ aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, @subjectid)
+ LOGGER.debug "Policy deleted for Dataset URI: #{uri} with result: #{aa}"
+ rescue
+ LOGGER.warn "Policy delete error for Dataset URI: #{uri}"
+ end
+ end
+ flash[:notice] = "#{model.name} model deleted."
+ rescue
+ flash[:notice] = "#{model.name} model delete error."
+ end
+ redirect url_for('/models')
end
delete '/?' do
- ToxCreateModel.auto_migrate!
- response['Content-Type'] = 'text/plain'
- "All Models deleted."
+ ToxCreateModel.all.each do |model|
+ begin
+ delete_model(model, @subjectid)
+ model.delete
+ unless ToxCreateModel.get(params[:id])
+ begin
+ aa = OpenTox::Authorization.delete_policies_from_uri(model.web_uri, @subjectid)
+ LOGGER.debug "Policy deleted for Dataset URI: #{uri} with result: #{aa}"
+ rescue
+ LOGGER.warn "Policy delete error for Dataset URI: #{uri}"
+ end
+ end
+ LOGGER.debug "#{model.name} model deleted."
+ rescue
+ LOGGER.error "#{model.name} model delete error."
+ end
+ end
+ response['Content-Type'] = 'text/plain'
+ "All Models deleted."
end
# SASS stylesheet
diff --git a/config.ru b/config.ru
index 78b1144..ec39d1b 100644
--- a/config.ru
+++ b/config.ru
@@ -1,5 +1,7 @@
require 'rubygems'
-require 'opentox-ruby-api-wrapper'
+require 'opentox-ruby'
require 'config/config_ru'
set :app_file, __FILE__ # to get the view path right
run Sinatra::Application
+set :raise_errors, false
+set :show_exceptions, false \ No newline at end of file
diff --git a/helper.rb b/helper.rb
index d100c9e..0813fff 100644
--- a/helper.rb
+++ b/helper.rb
@@ -1,5 +1,42 @@
helpers do
+ def login(username, password)
+ logout
+ session[:subjectid] = OpenTox::Authorization.authenticate(username, password)
+ LOGGER.debug "ToxCreate login user #{username} with subjectid: " + session[:subjectid].to_s
+ if session[:subjectid] != nil
+ session[:username] = username
+ return true
+ else
+ session[:username] = ""
+ return false
+ end
+ end
+
+ def logout
+ if session[:subjectid] != nil
+ session[:subjectid] = nil
+ session[:username] = ""
+ return true
+ end
+ return false
+ end
+
+ def logged_in()
+ return true if !AA_SERVER
+ if session[:subjectid] != nil
+ return OpenTox::Authorization.is_token_valid(session[:subjectid])
+ end
+ return false
+ end
+
+ def is_authorized(uri, action)
+ if session[:subjectid] != nil
+ return OpenTox::Authorization.authorize(uri, action, session[:subjectid])
+ end
+ return false
+ end
+
def hide_link(destination)
@link_id = 0 unless @link_id
@link_id += 1
@@ -12,8 +49,15 @@ helpers do
haml :js_link, :locals => {:name => name, :destination => destination, :method => "toggle"}, :layout => false
end
- def compound_image(compound,features)
- haml :compound_image, :locals => {:compound => compound, :features => features}, :layout => false
+ def sort(descriptors)
+ features = {:activating => [], :deactivating => []}
+
+ descriptors.each { |d| LOGGER.debug d.inspect; features[d[OT.effect].to_sym] << {:smarts => d[OT.smarts],:p_value => d[OT.pValue]} }
+ features
+ end
+
+ def compound_image(compound,descriptors)
+ haml :compound_image, :locals => {:compound => compound, :features => sort(descriptors)}, :layout => false
end
def activity_markup(activity)
diff --git a/model.rb b/model.rb
index 99d6ab3..7d22a4d 100644
--- a/model.rb
+++ b/model.rb
@@ -1,38 +1,93 @@
-class ToxCreateModel
-
- include DataMapper::Resource
- property :id, Serial
- property :name, String, :length => 255
- property :uri, String, :length => 255
- property :task_uri, String, :length => 255
- property :validation_task_uri, String, :length => 255
- property :validation_uri, String, :length => 255
- property :validation_report_task_uri, String, :length => 255
- property :validation_report_uri, String, :length => 255
- property :warnings, Text, :length => 2**32-1
- property :nr_compounds, Integer
- property :nr_predictions, Integer
- property :true_positives, Integer
- property :false_positives, Integer
- property :true_negatives, Integer
- property :false_negatives, Integer
- property :correct_predictions, Integer
- property :weighted_area_under_roc, Float
- property :sensitivity, Float
- property :specificity, Float
- property :r_square, Float
- property :root_mean_squared_error, Float
- property :mean_absolute_error, Float
- property :type, String
- property :created_at, DateTime
-
- def status
+require 'ohm'
+#require 'redis/objects'
+#@@redis = Redis.new(:thread_safe=>true)#(:host => '127.0.0.1', :port => 6379)
+
+class ToxCreateModel < Ohm::Model
+
+ #include Redis::Objects
+ #include DataMapper::Resource
+ #attribute :id
+ attribute :name
+ attribute :warnings
+ attribute :error_messages
+ attribute :type
+ attribute :status
+ attribute :created_at
+
+ attribute :task_uri
+ attribute :uri
+
+ attribute :training_dataset
+ attribute :feature_dataset
+ #attributey :validation_task_uri
+ attribute :validation_uri
+
+ #attributey :validation_report_task_uri
+ attribute :validation_report_uri
+
+ #attributey :validation_qmrf_task_uri
+ attribute :validation_qmrf_uri
+
+ attribute :nr_compounds
+ attribute :nr_predictions
+ attribute :true_positives
+ attribute :false_positives
+ attribute :true_negatives
+ attribute :false_negatives
+ attribute :correct_predictions
+ attribute :weighted_area_under_roc
+ attribute :sensitivity
+ attribute :specificity
+ attribute :r_square
+ attribute :root_mean_squared_error
+ attribute :mean_absolute_error
+
+ attribute :web_uri
+
+ attr_accessor :subjectid
+ @subjectid = nil
+
+ #after :save, :check_policy
+
+=begin
+ attr_accessor :id, :name, :warnings, :error_messages, :type, :status, :created_at, :task_uri, :uri, :training_dataset, :feature_dataset, :validation_task_uri, :validation_uri, :validation_report_task_uri, :validation_report_uri, :validation_qmrf_task_uri, :validation_qmrf_uri, :nr_compounds, :nr_predictions, :true_positives, :false_positives, :true_negatives, :false_negatives, :correct_predictions, :weighted_area_under_roc, :sensitivity, :specificity, :r_square, :root_mean_squared_error, :mean_absolute_error, :web_uri
+
+ def self.all
+ end
+
+ def self.get(id)
+ end
+
+ def self.create(params)
+ @id = @@redis.incr "toxcreate"
+ params.each { |k,v| @@redis.hset "toxcreate:#{@id}", k, v }
+ self.get(@id)
+ end
+
+ def update(params)
+ end
+
+ def method_missing
+ begin
+ rescue
+ raise "Unknown method"
+ end
+ end
+
+ attr_accessor :subjectid
+ @subjectid = nil
+
+ after :save, :check_policy
+
+def status
#begin
RestClient.get(File.join(@task_uri, 'hasStatus')).body
#rescue
# "Service offline"
#end
end
+=end
+=begin
def validation_status
begin
@@ -50,6 +105,14 @@ class ToxCreateModel
end
end
+ def validation_qmrf_status
+ begin
+ RestClient.get(File.join(@validation_qmrf_task_uri, 'hasStatus')).body
+ rescue
+ "Service offline"
+ end
+ end
+
def algorithm
begin
RestClient.get(File.join(@uri, 'algorithm')).body
@@ -74,87 +137,30 @@ class ToxCreateModel
end
end
-=begin
- def classification_validation
- begin
- uri = File.join(@validation_uri, 'statistics')
- yaml = RestClient.get(uri).body
- v = YAML.load(yaml)
- tp=0; tn=0; fp=0; fn=0; n=0
- v[:classification_statistics][:confusion_matrix][:confusion_matrix_cell].each do |cell|
- if cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "true"
- tp = cell[:confusion_matrix_value]
- n += tp
- elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "false"
- tn = cell[:confusion_matrix_value]
- n += tn
- elsif cell[:confusion_matrix_predicted] == "false" and cell[:confusion_matrix_actual] == "true"
- fn = cell[:confusion_matrix_value]
- n += fn
- elsif cell[:confusion_matrix_predicted] == "true" and cell[:confusion_matrix_actual] == "false"
- fp = cell[:confusion_matrix_value]
- n += fp
- end
- end
- @nr_predictions = n
- @true_positives = tp
- @false_positives = fp
- @true_negatives = tn
- @false_negatives = fn
- @correct_predictions = 100*(tp+tn).to_f/n
- @weighted_area_under_roc = v[:classification_statistics][:weighted_area_under_roc].to_f
- @sensitivity = tp.to_f/(tp+fn)
- @specificity = tn.to_f/(tn+fp)
- save
- #:correct_predictions => sprintf("%.2f", 100*(tp+tn).to_f/n),
- #:weighted_area_under_roc => sprintf("%.3f", v[:classification_statistics][:weighted_area_under_roc].to_f),
- #:sensitivity => sprintf("%.3f", tp.to_f/(tp+fn)),
- #:specificity => sprintf("%.3f", tn.to_f/(tn+fp))
- #}
- rescue
- "Service offline"
- end
- end
-
- def regression_validation
- begin
- uri = File.join(@validation_uri, 'statistics')
- yaml = RestClient.get(uri).body
- v = YAML.load(yaml)
- @nr_predictions = v[:num_instances] - v[:num_unpredicted]
- @r_square = v[:regression_statistics][:r_square]
- @root_mean_squared_error = v[:regression_statistics][:root_mean_squared_error]
- @mean_absolute_error = v[:regression_statistics][:mean_absolute_error]
- save
- rescue
- "Service offline"
- end
- end
-=end
-
def process
+ LOGGER.debug self.to_yaml
+
if @uri.nil? and status == "Completed"
- update :uri => RestClient.get(File.join(@task_uri, 'resultURI')).body
- lazar = YAML.load(RestClient.get(@uri, :accept => "application/x-yaml").body)
- case lazar.dependentVariables
- when /classification/
- update :type => "classification"
- when /regression/
- update :type => "regression"
- else
- update :type => "unknown"
- end
+ #update :uri => RestClient.get(File.join(@task_uri, 'resultURI')).body
+ #lazar = YAML.load(RestClient.get(@uri, :accept => "application/x-yaml").body)
elsif @validation_uri.nil? and validation_status == "Completed"
begin
- update :validation_uri => RestClient.get(File.join(@validation_task_uri, 'resultURI')).body
- LOGGER.debug "Validation URI: #{@validation_uri}"
- update :validation_report_task_uri => RestClient.post(File.join(@@config[:services]["opentox-validation"],"/report/crossvalidation"), :validation_uris => @validation_uri).body
- LOGGER.debug "Validation Report Task URI: #{@validation_report_task_uri}"
+
+ #update :validation_uri => RestClient.get(File.join(@validation_task_uri, 'resultURI')).body
+ #LOGGER.debug "Validation URI: #{@validation_uri}"
+
+ #update :validation_report_task_uri => RestClient.post(File.join(CONFIG[:services]["opentox-validation"],"/report/crossvalidation"), :validation_uris => @validation_uri).body
+ #LOGGER.debug "Validation Report Task URI: #{@validation_report_task_uri}"
+
+ #update :validation_qmrf_task_uri => RestClient.post(File.join(CONFIG[:services]["opentox-validation"],"/reach_report/qmrf"), :model_uri => @uri).body
+ #LOGGER.debug "QMRF Report Task URI: #{@validation_qmrf_task_uri}"
+
uri = File.join(@validation_uri, 'statistics')
yaml = RestClient.get(uri).body
v = YAML.load(yaml)
+
case type
when "classification"
tp=0; tn=0; fp=0; fn=0; n=0
@@ -192,18 +198,34 @@ class ToxCreateModel
LOGGER.warn "Cannot create Validation Report Task #{@validation_report_task_uri} for Validation URI #{@validation_uri} from Task #{@validation_task_uri}"
end
- elsif @validation_report_uri.nil? and validation_report_status == "Completed"
- begin
- LOGGER.debug File.join(@validation_report_task_uri, 'resultURI')
- LOGGER.debug "Report URI: "+RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
- update :validation_report_uri => RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
- rescue
- LOGGER.warn "Cannot create Validation Report for Task URI #{@validation_report_task_uri} "
- end
- end
+ else
+
+ if @validation_report_uri.nil? and validation_report_status == "Completed"
+ begin
+ update :validation_report_uri => RestClient.get(File.join(@validation_report_task_uri, 'resultURI')).body
+ rescue
+ LOGGER.warn "Cannot create Validation Report for Task URI #{@validation_report_task_uri} "
+ end
+ end
+
+ if @validation_qmrf_uri.nil? and validation_qmrf_status == "Completed"
+ begin
+ update :validation_qmrf_uri => RestClient.get(File.join(@validation_qmrf_task_uri, 'resultURI')).body
+ rescue
+ LOGGER.warn "Cannot create QMRF Report for Task URI #{@validation_qmrf_task_uri} "
+ end
+ end
+
+ end
+
+ end
+=end
+ private
+ def check_policy
+ OpenTox::Authorization.check_policy(web_uri, subjectid)
end
end
-DataMapper.auto_upgrade!
+#DataMapper.auto_upgrade!
diff --git a/parser.rb b/parser.rb
deleted file mode 100644
index 8468cea..0000000
--- a/parser.rb
+++ /dev/null
@@ -1,119 +0,0 @@
-require 'spreadsheet'
-require 'roo'
-class Parser
-
- attr_accessor :dataset, :format_errors, :smiles_errors, :activity_errors, :duplicates, :nr_compounds, :dataset_uri
-
- def initialize(file, endpoint_uri)
-
- @file = file
- @dataset = OpenTox::Dataset.new
- @feature_uri = endpoint_uri
- @dataset.features << endpoint_uri
- @dataset.title = URI.decode(endpoint_uri.split(/#/).last)
- @format_errors = ""
- @smiles_errors = []
- @activity_errors = []
- @duplicates = {}
- @nr_compounds = 0
- @data = []
- @activities = []
- @type = "classification"
-
- # check format by extension - not all browsers provide correct content-type])
- case File.extname(@file[:filename])
- when ".csv"
- self.csv
- when ".xls", ".xlsx"
- self.excel
- else
- @format_errors = "#{@file[:filename]} is a unsupported file type."
- return false
- end
-
- # create dataset
- @data.each do |items|
- @dataset.compounds << items[0]
- @dataset.data[items[0]] = [] unless @dataset.data[items[0]]
- case @type
- when "classification"
- case items[1].to_s
- when TRUE_REGEXP
- @dataset.data[items[0]] << {@feature_uri => true }
- when FALSE_REGEXP
- @dataset.data[items[0]] << {@feature_uri => false }
- end
- when "regression"
- if items[1].to_f == 0
- @activity_errors << "Row #{items[2]}: Zero values not allowed for regression datasets - entry ignored."
- else
- @dataset.data[items[0]] << {@feature_uri => items[1].to_f}
- end
- end
- end
- @dataset_uri = @dataset.save
-
- end
-
- def csv
- row = 0
- @file[:tempfile].each_line do |line|
- row += 1
- unless line.chomp.match(/^.+[,;].*$/) # check CSV format
- @format_errors = "#{@file[:filename]} is not a valid CSV file."
- return false
- end
- items = line.chomp.gsub(/["']/,'').split(/\s*[,;]\s*/) # remove quotes
- LOGGER.debug items.join(",")
- input = validate(items[0], items[1], row) # smiles, activity
- @data << input if input
- end
- end
-
- def excel
- excel = 'tmp/' + @file[:filename]
- File.mv(@file[:tempfile].path,excel)
- begin
- if File.extname(@file[:filename]) == ".xlsx"
- book = Excelx.new(excel)
- else
- book = Excel.new(excel)
- end
- book.default_sheet = 0
- 1.upto(book.last_row) do |row|
- input = validate( book.cell(row,1), book.cell(row,2), row ) # smiles, activity
- @data << input if input
- end
- File.safe_unlink(@file[:tempfile])
- rescue
- @format_errors = "#{@file[:filename]} is not a valid Excel input file."
- return false
- end
- end
-
- def validate(smiles, act, row)
- compound = OpenTox::Compound.new(:smiles => smiles)
- if compound.nil? or compound.inchi.nil? or compound.inchi == ""
- @smiles_errors << "Row #{row}: " + [smiles,act].join(", ")
- return false
- end
- unless numeric?(act) or classification?(act)
- @activity_errors << "Row #{row}: " + [smiles,act].join(", ")
- return false
- end
- @duplicates[compound.inchi] = [] unless @duplicates[compound.inchi]
- @duplicates[compound.inchi] << "Row #{row}: " + [smiles, act].join(", ")
- @type = "regression" unless classification?(act)
- @nr_compounds += 1
- [ compound.uri, act , row ]
- end
-
- def numeric?(object)
- true if Float(object) rescue false
- end
-
- def classification?(object)
- !object.to_s.strip.match(TRUE_REGEXP).nil? or !object.to_s.strip.match(FALSE_REGEXP).nil?
- end
-
-end
diff --git a/public/javascripts/jquery-ui-progressbar.js b/public/javascripts/jquery-ui-progressbar.js
new file mode 100644
index 0000000..64c2a2c
--- /dev/null
+++ b/public/javascripts/jquery-ui-progressbar.js
@@ -0,0 +1,49 @@
+/*!
+ * jQuery UI 1.8.9
+ *
+ * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * http://docs.jquery.com/UI
+ */
+(function(c,j){function k(a){return!c(a).parents().andSelf().filter(function(){return c.curCSS(this,"visibility")==="hidden"||c.expr.filters.hidden(this)}).length}c.ui=c.ui||{};if(!c.ui.version){c.extend(c.ui,{version:"1.8.9",keyCode:{ALT:18,BACKSPACE:8,CAPS_LOCK:20,COMMA:188,COMMAND:91,COMMAND_LEFT:91,COMMAND_RIGHT:93,CONTROL:17,DELETE:46,DOWN:40,END:35,ENTER:13,ESCAPE:27,HOME:36,INSERT:45,LEFT:37,MENU:93,NUMPAD_ADD:107,NUMPAD_DECIMAL:110,NUMPAD_DIVIDE:111,NUMPAD_ENTER:108,NUMPAD_MULTIPLY:106,
+NUMPAD_SUBTRACT:109,PAGE_DOWN:34,PAGE_UP:33,PERIOD:190,RIGHT:39,SHIFT:16,SPACE:32,TAB:9,UP:38,WINDOWS:91}});c.fn.extend({_focus:c.fn.focus,focus:function(a,b){return typeof a==="number"?this.each(function(){var d=this;setTimeout(function(){c(d).focus();b&&b.call(d)},a)}):this._focus.apply(this,arguments)},scrollParent:function(){var a;a=c.browser.msie&&/(static|relative)/.test(this.css("position"))||/absolute/.test(this.css("position"))?this.parents().filter(function(){return/(relative|absolute|fixed)/.test(c.curCSS(this,
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+if(b==="absolute"||b==="relative"||b==="fixed"){b=parseInt(a.css("zIndex"),10);if(!isNaN(b)&&b!==0)return b}a=a.parent()}}return 0},disableSelection:function(){return this.bind((c.support.selectstart?"selectstart":"mousedown")+".ui-disableSelection",function(a){a.preventDefault()})},enableSelection:function(){return this.unbind(".ui-disableSelection")}});c.each(["Width","Height"],function(a,b){function d(f,g,l,m){c.each(e,function(){g-=parseFloat(c.curCSS(f,"padding"+this,true))||0;if(l)g-=parseFloat(c.curCSS(f,
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+c(function(){var a=document.body,b=a.appendChild(b=document.createElement("div"));c.extend(b.style,{minHeight:"100px",height:"auto",padding:0,borderWidth:0});c.support.minHeight=b.offsetHeight===100;c.support.selectstart="onselectstart"in b;a.removeChild(b).style.display="none"});c.extend(c.ui,{plugin:{add:function(a,b,d){a=c.ui[a].prototype;for(var e in d){a.plugins[e]=a.plugins[e]||[];a.plugins[e].push([b,d[e]])}},call:function(a,b,d){if((b=a.plugins[b])&&a.element[0].parentNode)for(var e=0;e<b.length;e++)a.options[b[e][0]]&&
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+;/*!
+ * jQuery UI Widget 1.8.9
+ *
+ * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * http://docs.jquery.com/UI/Widget
+ */
+(function(b,j){if(b.cleanData){var k=b.cleanData;b.cleanData=function(a){for(var c=0,d;(d=a[c])!=null;c++)b(d).triggerHandler("remove");k(a)}}else{var l=b.fn.remove;b.fn.remove=function(a,c){return this.each(function(){if(!c)if(!a||b.filter(a,[this]).length)b("*",this).add([this]).each(function(){b(this).triggerHandler("remove")});return l.call(b(this),a,c)})}}b.widget=function(a,c,d){var e=a.split(".")[0],f;a=a.split(".")[1];f=e+"-"+a;if(!d){d=c;c=b.Widget}b.expr[":"][f]=function(h){return!!b.data(h,
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+widget:function(){return this.element},option:function(a,c){var d=a;if(arguments.length===0)return b.extend({},this.options);if(typeof a==="string"){if(c===j)return this.options[a];d={};d[a]=c}this._setOptions(d);return this},_setOptions:function(a){var c=this;b.each(a,function(d,e){c._setOption(d,e)});return this},_setOption:function(a,c){this.options[a]=c;if(a==="disabled")this.widget()[c?"addClass":"removeClass"](this.widgetBaseClass+"-disabled ui-state-disabled").attr("aria-disabled",c);return this},
+enable:function(){return this._setOption("disabled",false)},disable:function(){return this._setOption("disabled",true)},_trigger:function(a,c,d){var e=this.options[a];c=b.Event(c);c.type=(a===this.widgetEventPrefix?a:this.widgetEventPrefix+a).toLowerCase();d=d||{};if(c.originalEvent){a=b.event.props.length;for(var f;a;){f=b.event.props[--a];c[f]=c.originalEvent[f]}}this.element.trigger(c,d);return!(b.isFunction(e)&&e.call(this.element[0],c,d)===false||c.isDefaultPrevented())}}})(jQuery);
+;/*
+ * jQuery UI Progressbar 1.8.9
+ *
+ * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * http://docs.jquery.com/UI/Progressbar
+ *
+ * Depends:
+ * jquery.ui.core.js
+ * jquery.ui.widget.js
+ */
+(function(b,d){b.widget("ui.progressbar",{options:{value:0,max:100},min:0,_create:function(){this.element.addClass("ui-progressbar ui-widget ui-widget-content ui-corner-all").attr({role:"progressbar","aria-valuemin":this.min,"aria-valuemax":this.options.max,"aria-valuenow":this._value()});this.valueDiv=b("<div class='ui-progressbar-value ui-widget-header ui-corner-left'></div>").appendTo(this.element);this.oldValue=this._value();this._refreshValue()},destroy:function(){this.element.removeClass("ui-progressbar ui-widget ui-widget-content ui-corner-all").removeAttr("role").removeAttr("aria-valuemin").removeAttr("aria-valuemax").removeAttr("aria-valuenow");
+this.valueDiv.remove();b.Widget.prototype.destroy.apply(this,arguments)},value:function(a){if(a===d)return this._value();this._setOption("value",a);return this},_setOption:function(a,c){if(a==="value"){this.options.value=c;this._refreshValue();this._value()===this.options.max&&this._trigger("complete")}b.Widget.prototype._setOption.apply(this,arguments)},_value:function(){var a=this.options.value;if(typeof a!=="number")a=0;return Math.min(this.options.max,Math.max(this.min,a))},_percentage:function(){return 100*
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+; \ No newline at end of file
diff --git a/public/javascripts/jquery.js b/public/javascripts/jquery.js
index 7c24308..8f3ca2e 100755..100644
--- a/public/javascripts/jquery.js
+++ b/public/javascripts/jquery.js
@@ -1,5 +1,5 @@
/*!
- * jQuery JavaScript Library v1.4.2
+ * jQuery JavaScript Library v1.4.4
* http://jquery.com/
*
* Copyright 2010, John Resig
@@ -11,144 +11,157 @@
* Copyright 2010, The Dojo Foundation
* Released under the MIT, BSD, and GPL Licenses.
*
- * Date: Sat Feb 13 22:33:48 2010 -0500
+ * Date: Thu Nov 11 19:04:53 2010 -0500
*/
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+f.offsetTop===5;e.style.position="fixed";e.style.top="20px";this.supportsFixedPosition=e.offsetTop===20||e.offsetTop===15;e.style.position=e.style.top="";d.style.overflow="hidden";d.style.position="relative";this.subtractsBorderForOverflowNotVisible=e.offsetTop===-5;this.doesNotIncludeMarginInBodyOffset=a.offsetTop!==h;a.removeChild(b);c.offset.initialize=c.noop},bodyOffset:function(a){var b=a.offsetTop,d=a.offsetLeft;c.offset.initialize();if(c.offset.doesNotIncludeMarginInBodyOffset){b+=parseFloat(c.css(a,
+"marginTop"))||0;d+=parseFloat(c.css(a,"marginLeft"))||0}return{top:b,left:d}},setOffset:function(a,b,d){var e=c.css(a,"position");if(e==="static")a.style.position="relative";var f=c(a),h=f.offset(),l=c.css(a,"top"),k=c.css(a,"left"),o=e==="absolute"&&c.inArray("auto",[l,k])>-1;e={};var x={};if(o)x=f.position();l=o?x.top:parseInt(l,10)||0;k=o?x.left:parseInt(k,10)||0;if(c.isFunction(b))b=b.call(a,d,h);if(b.top!=null)e.top=b.top-h.top+l;if(b.left!=null)e.left=b.left-h.left+k;"using"in b?b.using.call(a,
+e):f.css(e)}};c.fn.extend({position:function(){if(!this[0])return null;var a=this[0],b=this.offsetParent(),d=this.offset(),e=Ia.test(b[0].nodeName)?{top:0,left:0}:b.offset();d.top-=parseFloat(c.css(a,"marginTop"))||0;d.left-=parseFloat(c.css(a,"marginLeft"))||0;e.top+=parseFloat(c.css(b[0],"borderTopWidth"))||0;e.left+=parseFloat(c.css(b[0],"borderLeftWidth"))||0;return{top:d.top-e.top,left:d.left-e.left}},offsetParent:function(){return this.map(function(){for(var a=this.offsetParent||t.body;a&&!Ia.test(a.nodeName)&&
+c.css(a,"position")==="static";)a=a.offsetParent;return a})}});c.each(["Left","Top"],function(a,b){var d="scroll"+b;c.fn[d]=function(e){var f=this[0],h;if(!f)return null;if(e!==B)return this.each(function(){if(h=fa(this))h.scrollTo(!a?e:c(h).scrollLeft(),a?e:c(h).scrollTop());else this[d]=e});else return(h=fa(f))?"pageXOffset"in h?h[a?"pageYOffset":"pageXOffset"]:c.support.boxModel&&h.document.documentElement[d]||h.document.body[d]:f[d]}});c.each(["Height","Width"],function(a,b){var d=b.toLowerCase();
+c.fn["inner"+b]=function(){return this[0]?parseFloat(c.css(this[0],d,"padding")):null};c.fn["outer"+b]=function(e){return this[0]?parseFloat(c.css(this[0],d,e?"margin":"border")):null};c.fn[d]=function(e){var f=this[0];if(!f)return e==null?null:this;if(c.isFunction(e))return this.each(function(l){var k=c(this);k[d](e.call(this,l,k[d]()))});if(c.isWindow(f))return f.document.compatMode==="CSS1Compat"&&f.document.documentElement["client"+b]||f.document.body["client"+b];else if(f.nodeType===9)return Math.max(f.documentElement["client"+
+b],f.body["scroll"+b],f.documentElement["scroll"+b],f.body["offset"+b],f.documentElement["offset"+b]);else if(e===B){f=c.css(f,d);var h=parseFloat(f);return c.isNaN(h)?f:h}else return this.css(d,typeof e==="string"?e:e+"px")}})})(window);
diff --git a/public/javascripts/toxcreate.js b/public/javascripts/toxcreate.js
index d1ed490..410778f 100755
--- a/public/javascripts/toxcreate.js
+++ b/public/javascripts/toxcreate.js
@@ -14,19 +14,24 @@ $(function() {
});
};
- checkStati = function(stati) {
- stati = stati.split(", ")
+ trim = function() {
+ return this.replace(/^\s+|\s+$/g, '');
+ }
+
+ checkStati = function(stati, subjectstr) {
+ stati = stati.split(", ");
$("body")
var newstati = new Array;
$.each(stati, function(){
- if(checkStatus(this) > 0) newstati.push(this);
+ checkProgress(this, subjectstr);
+ if(checkStatus(this, subjectstr) > 0) newstati.push(this);
});
- if (newstati.length > 0) var statusCheck = setTimeout('checkStati("' + newstati.join(", ") + '")',10000);
+ if (newstati.length > 0) var statusCheck = setTimeout('checkStati("' + newstati.join(", ") + '", "' + subjectstr + '")',10000);
};
- checkStatus = function(id) {
+ checkStatus = function(id, subjectstr) {
if(id == "") return -1;
- var opts = {method: 'get', action: 'model/' + id + '/status', id: id};
+ var opts = {method: 'get', action: 'model/' + id + '/status' + subjectstr, id: id};
var status_changed = $.ajax({
type: opts.method,
url: opts.action,
@@ -36,15 +41,16 @@ $(function() {
'_method': 'get'
},
success: function(data) {
- var erg = data.search(/Running/);
- status_changed = false;
- if(erg < 0) status_changed = true;
- $("span#model_" + id + "_status").animate({"opacity": "0.1"},1000);
+ var status_before = "";
+ if ($("span#model_" + id + "_status") != null) status_before = $("span#model_" + id + "_status").html().trim();
+ if (status_before == "Deleting") return -1;
+ var status_after = data.trim();
+ $("span#model_" + id + "_status").animate({"opacity": "0.2"},1000);
$("span#model_" + id + "_status").animate({"opacity": "1"},1000);
- if( status_changed ) {
+ if( status_before != status_after) {
$("span#model_" + id + "_status").html(data);
loadModel(id, 'model');
- id = -1;
+ if (status_after == "Completed") id = -1;
}
},
error: function(data) {
@@ -54,6 +60,34 @@ $(function() {
});
return id;
};
+
+
+ checkProgress = function(id, subjectstr) {
+ var task = $("input#model_" + id + "_task").attr('value');
+ var opts = {action: task + "/percentageCompleted" , id: id};
+ var progress_changed = $.ajax({
+ url: opts.action,
+ async: false,
+ dataType: 'html',
+ data: {
+ '_method': 'get'
+ },
+ success: function(data) {
+ var progress = data.trim();
+ if (progress == "100") return -1;
+
+ $("div#model_" + id + "_progress").progressbar("value", parseInt(progress));
+ $("div#model_" + id + "_progress").attr({title: parseInt(progress) + "%", alt: parseInt(progress) + "%"});
+ //$("div#model_" + id + "_progress").attr("alt", parseInt(progress) + "%");
+ },
+ error: function(data) {
+ id = -1;
+ }
+ });
+ return id;
+ };
+
+
loadModel = function(id, view) {
if(id == "") return -1;
@@ -85,10 +119,68 @@ $(function() {
if(/^\d+$/.test(reload_id)) loadModel(reload_id, 'validation');
};
});
- var validationCheck = setTimeout('checkValidation()',15000);
+ //var validationCheck = setTimeout('checkValidation()',15000);
+ var validationCheck = setTimeout('checkValidation()',5000);
}
});
+jQuery.fn.editModel = function(type, options) {
+ var defaults = {
+ method: 'get',
+ action: this.attr('href'),
+ trigger_on: 'click'
+ };
+ var opts = $.extend(defaults, options);
+ this.bind(opts.trigger_on, function() {
+ $.ajax({
+ type: opts.method,
+ url: opts.action,
+ dataType: 'html',
+ data: {
+ '_method': 'get'
+ },
+ success: function(data) {
+ $("div#model_" + opts.id + "_name").html(data);
+ $("input#model_" + opts.id + "_name").focus();
+ },
+ error: function(data) {
+ alert("model edit error!");
+ }
+ });
+ return false;
+ });
+};
+
+jQuery.fn.saveModel = function(type, options) {
+ var defaults = {
+ method: 'put',
+ action: 'model/' + options.id,
+ trigger_on: 'click'
+ };
+ var opts = $.extend(defaults, options);
+
+ this.bind(opts.trigger_on, function() {
+ var name = $("input#model_" + opts.id + "_name").val();
+ $.ajax({
+ type: opts.method,
+ url: opts.action,
+ dataType: 'html',
+ data: {
+ '_method': 'put',
+ 'name': name
+ },
+ success: function(data) {
+ $("div#model_" + opts.id + "_name").html(data);
+ },
+ error: function(data) {
+ alert("model save error!");
+ }
+ });
+ return false;
+ });
+};
+
+
jQuery.fn.deleteModel = function(type, options) {
var defaults = {
method: 'post',
@@ -99,7 +191,8 @@ jQuery.fn.deleteModel = function(type, options) {
var opts = $.extend(defaults, options);
this.bind(opts.trigger_on, function() {
if(confirm(opts.confirm_message)) {
- $(opts.elem).fadeTo("slow",0.5);
+ $("div#model_" + opts.id).fadeTo("slow",0.5);
+ $("span#model_" + opts.id + "_status").html("Deleting");
$.ajax({
type: opts.method,
url: opts.action,
@@ -108,9 +201,10 @@ jQuery.fn.deleteModel = function(type, options) {
'_method': 'delete'
},
success: function(data) {
- $(opts.elem).fadeTo("slow",0).slideUp("slow").remove();
+ $("div#model_" + opts.id).fadeTo("slow",0).slideUp("slow").remove();
},
error: function(data) {
+ $("span#model_" + opts.id + "_status").html("Delete Error");
//alert("model delete error!");
}
});
diff --git a/public/progressbar/images/ui-bg_flat_0_aaaaaa_40x100.png b/public/progressbar/images/ui-bg_flat_0_aaaaaa_40x100.png
new file mode 100644
index 0000000..f4b49ad
--- /dev/null
+++ b/public/progressbar/images/ui-bg_flat_0_aaaaaa_40x100.png
Binary files differ
diff --git a/public/progressbar/images/ui-bg_glass_95_fef1ec_1x400.png b/public/progressbar/images/ui-bg_glass_95_fef1ec_1x400.png
new file mode 100644
index 0000000..4443fdc
--- /dev/null
+++ b/public/progressbar/images/ui-bg_glass_95_fef1ec_1x400.png
Binary files differ
diff --git a/public/progressbar/images/ui-bg_gloss-wave_16_121212_500x100.png b/public/progressbar/images/ui-bg_gloss-wave_16_121212_500x100.png
new file mode 100644
index 0000000..a2371bf
--- /dev/null
+++ b/public/progressbar/images/ui-bg_gloss-wave_16_121212_500x100.png
Binary files differ
diff --git a/public/progressbar/images/ui-bg_highlight-hard_15_888888_1x100.png b/public/progressbar/images/ui-bg_highlight-hard_15_888888_1x100.png
new file mode 100644
index 0000000..7a61a4d
--- /dev/null
+++ b/public/progressbar/images/ui-bg_highlight-hard_15_888888_1x100.png
Binary files differ
diff --git a/public/progressbar/images/ui-bg_highlight-hard_55_555555_1x100.png b/public/progressbar/images/ui-bg_highlight-hard_55_555555_1x100.png
new file mode 100644
index 0000000..1453bc1
--- /dev/null
+++ b/public/progressbar/images/ui-bg_highlight-hard_55_555555_1x100.png
Binary files differ
diff --git a/public/progressbar/images/ui-bg_highlight-soft_35_adadad_1x100.png b/public/progressbar/images/ui-bg_highlight-soft_35_adadad_1x100.png
new file mode 100644
index 0000000..5a5a41d
--- /dev/null
+++ b/public/progressbar/images/ui-bg_highlight-soft_35_adadad_1x100.png
Binary files differ
diff --git a/public/progressbar/images/ui-bg_highlight-soft_60_dddddd_1x100.png b/public/progressbar/images/ui-bg_highlight-soft_60_dddddd_1x100.png
new file mode 100644
index 0000000..747e1fa
--- /dev/null
+++ b/public/progressbar/images/ui-bg_highlight-soft_60_dddddd_1x100.png
Binary files differ
diff --git a/public/progressbar/images/ui-bg_inset-soft_15_121212_1x100.png b/public/progressbar/images/ui-bg_inset-soft_15_121212_1x100.png
new file mode 100644
index 0000000..9df26a0
--- /dev/null
+++ b/public/progressbar/images/ui-bg_inset-soft_15_121212_1x100.png
Binary files differ
diff --git a/public/progressbar/images/ui-icons_666666_256x240.png b/public/progressbar/images/ui-icons_666666_256x240.png
new file mode 100644
index 0000000..f87de1c
--- /dev/null
+++ b/public/progressbar/images/ui-icons_666666_256x240.png
Binary files differ
diff --git a/public/progressbar/images/ui-icons_aaaaaa_256x240.png b/public/progressbar/images/ui-icons_aaaaaa_256x240.png
new file mode 100644
index 0000000..64af7f1
--- /dev/null
+++ b/public/progressbar/images/ui-icons_aaaaaa_256x240.png
Binary files differ
diff --git a/public/progressbar/images/ui-icons_bbbbbb_256x240.png b/public/progressbar/images/ui-icons_bbbbbb_256x240.png
new file mode 100644
index 0000000..9d71edb
--- /dev/null
+++ b/public/progressbar/images/ui-icons_bbbbbb_256x240.png
Binary files differ
diff --git a/public/progressbar/images/ui-icons_c98000_256x240.png b/public/progressbar/images/ui-icons_c98000_256x240.png
new file mode 100644
index 0000000..ba8dafc
--- /dev/null
+++ b/public/progressbar/images/ui-icons_c98000_256x240.png
Binary files differ
diff --git a/public/progressbar/images/ui-icons_cccccc_256x240.png b/public/progressbar/images/ui-icons_cccccc_256x240.png
new file mode 100644
index 0000000..9254e05
--- /dev/null
+++ b/public/progressbar/images/ui-icons_cccccc_256x240.png
Binary files differ
diff --git a/public/progressbar/images/ui-icons_cd0a0a_256x240.png b/public/progressbar/images/ui-icons_cd0a0a_256x240.png
new file mode 100644
index 0000000..2ab019b
--- /dev/null
+++ b/public/progressbar/images/ui-icons_cd0a0a_256x240.png
Binary files differ
diff --git a/public/progressbar/images/ui-icons_f29a00_256x240.png b/public/progressbar/images/ui-icons_f29a00_256x240.png
new file mode 100644
index 0000000..540e43b
--- /dev/null
+++ b/public/progressbar/images/ui-icons_f29a00_256x240.png
Binary files differ
diff --git a/public/progressbar/progressbar.css b/public/progressbar/progressbar.css
new file mode 100644
index 0000000..92e3f82
--- /dev/null
+++ b/public/progressbar/progressbar.css
@@ -0,0 +1,305 @@
+/*
+ * jQuery UI CSS Framework 1.8.9
+ *
+ * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * http://docs.jquery.com/UI/Theming/API
+ */
+
+/* Layout helpers
+----------------------------------*/
+.ui-helper-hidden { display: none; }
+.ui-helper-hidden-accessible { position: absolute !important; clip: rect(1px 1px 1px 1px); clip: rect(1px,1px,1px,1px); }
+.ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-height: 1.3; text-decoration: none; font-size: 100%; list-style: none; }
+.ui-helper-clearfix:after { content: "."; display: block; height: 0; clear: both; visibility: hidden; }
+.ui-helper-clearfix { display: inline-block; }
+/* required comment for clearfix to work in Opera \*/
+* html .ui-helper-clearfix { height:1%; }
+.ui-helper-clearfix { display:block; }
+/* end clearfix */
+.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: absolute; opacity: 0; filter:Alpha(Opacity=0); }
+
+
+/* Interaction Cues
+----------------------------------*/
+.ui-state-disabled { cursor: default !important; }
+
+
+/* Icons
+----------------------------------*/
+
+/* states and images */
+.ui-icon { display: block; text-indent: -99999px; overflow: hidden; background-repeat: no-repeat; }
+
+
+/* Misc visuals
+----------------------------------*/
+
+/* Overlays */
+.ui-widget-overlay { position: absolute; top: 0; left: 0; width: 100%; height: 100%; }
+
+
+/*
+ * jQuery UI CSS Framework 1.8.9
+ *
+ * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * http://docs.jquery.com/UI/Theming/API
+ *
+ * To view and modify this theme, visit http://jqueryui.com/themeroller/?tr&ffDefault=Helvetica,%20Arial,%20sans-serif&fwDefault=normal&fsDefault=1.1&fsDefaultUnit=em&cornerRadius=5&cornerRadiusUnit=px&bgColorHeader=888888&bgTextureHeader=04_highlight_hard.png&bgImgOpacityHeader=15&borderColorHeader=404040&fcHeader=ffffff&iconColorHeader=cccccc&bgColorContent=121212&bgTextureContent=12_gloss_wave.png&bgImgOpacityContent=16&borderColorContent=404040&fcContent=eeeeee&iconColorContent=bbbbbb&bgColorDefault=adadad&bgTextureDefault=03_highlight_soft.png&bgImgOpacityDefault=35&borderColorDefault=cccccc&fcDefault=333333&iconColorDefault=666666&bgColorHover=dddddd&bgTextureHover=03_highlight_soft.png&bgImgOpacityHover=60&borderColorHover=dddddd&fcHover=000000&iconColorHover=c98000&bgColorActive=121212&bgTextureActive=05_inset_soft.png&bgImgOpacityActive=15&borderColorActive=000000&fcActive=ffffff&iconColorActive=f29a00&bgColorHighlight=555555&bgTextureHighlight=04_highlight_hard.png&bgImgOpacityHighlight=55&borderColorHighlight=404040&fcHighlight=cccccc&iconColorHighlight=aaaaaa&bgColorError=fef1ec&bgTextureError=02_glass.png&bgImgOpacityError=95&borderColorError=cd0a0a&fcError=cd0a0a&iconColorError=cd0a0a
+ */
+
+
+/* Component containers
+----------------------------------*/
+.ui-widget { font-family: Helvetica, Arial, sans-serif; font-size: 1.1em; }
+.ui-widget .ui-widget { font-size: 1em; }
+.ui-widget input, .ui-widget select, .ui-widget textarea, .ui-widget button { font-family: Helvetica, Arial, sans-serif; font-size: 1em; }
+.ui-widget-content { border: 1px solid #404040; background: #121212 url(images/ui-bg_gloss-wave_16_121212_500x100.png) 50% top repeat-x; color: #eeeeee; }
+.ui-widget-content a { color: #eeeeee; }
+.ui-widget-header { border: 1px solid #404040; background: #888888 url(images/ui-bg_highlight-hard_15_888888_1x100.png) 50% 50% repeat-x; color: #ffffff; font-weight: bold; }
+.ui-widget-header a { color: #ffffff; }
+
+/* Interaction states
+----------------------------------*/
+.ui-state-default, .ui-widget-content .ui-state-default, .ui-widget-header .ui-state-default { border: 1px solid #cccccc; background: #adadad url(images/ui-bg_highlight-soft_35_adadad_1x100.png) 50% 50% repeat-x; font-weight: normal; color: #333333; }
+.ui-state-default a, .ui-state-default a:link, .ui-state-default a:visited { color: #333333; text-decoration: none; }
+.ui-state-hover, .ui-widget-content .ui-state-hover, .ui-widget-header .ui-state-hover, .ui-state-focus, .ui-widget-content .ui-state-focus, .ui-widget-header .ui-state-focus { border: 1px solid #dddddd; background: #dddddd url(images/ui-bg_highlight-soft_60_dddddd_1x100.png) 50% 50% repeat-x; font-weight: normal; color: #000000; }
+.ui-state-hover a, .ui-state-hover a:hover { color: #000000; text-decoration: none; }
+.ui-state-active, .ui-widget-content .ui-state-active, .ui-widget-header .ui-state-active { border: 1px solid #000000; background: #121212 url(images/ui-bg_inset-soft_15_121212_1x100.png) 50% 50% repeat-x; font-weight: normal; color: #ffffff; }
+.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited { color: #ffffff; text-decoration: none; }
+.ui-widget :active { outline: none; }
+
+/* Interaction Cues
+----------------------------------*/
+.ui-state-highlight, .ui-widget-content .ui-state-highlight, .ui-widget-header .ui-state-highlight {border: 1px solid #404040; background: #555555 url(images/ui-bg_highlight-hard_55_555555_1x100.png) 50% top repeat-x; color: #cccccc; }
+.ui-state-highlight a, .ui-widget-content .ui-state-highlight a,.ui-widget-header .ui-state-highlight a { color: #cccccc; }
+.ui-state-error, .ui-widget-content .ui-state-error, .ui-widget-header .ui-state-error {border: 1px solid #cd0a0a; background: #fef1ec url(images/ui-bg_glass_95_fef1ec_1x400.png) 50% 50% repeat-x; color: #cd0a0a; }
+.ui-state-error a, .ui-widget-content .ui-state-error a, .ui-widget-header .ui-state-error a { color: #cd0a0a; }
+.ui-state-error-text, .ui-widget-content .ui-state-error-text, .ui-widget-header .ui-state-error-text { color: #cd0a0a; }
+.ui-priority-primary, .ui-widget-content .ui-priority-primary, .ui-widget-header .ui-priority-primary { font-weight: bold; }
+.ui-priority-secondary, .ui-widget-content .ui-priority-secondary, .ui-widget-header .ui-priority-secondary { opacity: .7; filter:Alpha(Opacity=70); font-weight: normal; }
+.ui-state-disabled, .ui-widget-content .ui-state-disabled, .ui-widget-header .ui-state-disabled { opacity: .35; filter:Alpha(Opacity=35); background-image: none; }
+
+/* Icons
+----------------------------------*/
+
+/* states and images */
+.ui-icon { width: 16px; height: 16px; background-image: url(images/ui-icons_bbbbbb_256x240.png); }
+.ui-widget-content .ui-icon {background-image: url(images/ui-icons_bbbbbb_256x240.png); }
+.ui-widget-header .ui-icon {background-image: url(images/ui-icons_cccccc_256x240.png); }
+.ui-state-default .ui-icon { background-image: url(images/ui-icons_666666_256x240.png); }
+.ui-state-hover .ui-icon, .ui-state-focus .ui-icon {background-image: url(images/ui-icons_c98000_256x240.png); }
+.ui-state-active .ui-icon {background-image: url(images/ui-icons_f29a00_256x240.png); }
+.ui-state-highlight .ui-icon {background-image: url(images/ui-icons_aaaaaa_256x240.png); }
+.ui-state-error .ui-icon, .ui-state-error-text .ui-icon {background-image: url(images/ui-icons_cd0a0a_256x240.png); }
+
+/* positioning */
+.ui-icon-carat-1-n { background-position: 0 0; }
+.ui-icon-carat-1-ne { background-position: -16px 0; }
+.ui-icon-carat-1-e { background-position: -32px 0; }
+.ui-icon-carat-1-se { background-position: -48px 0; }
+.ui-icon-carat-1-s { background-position: -64px 0; }
+.ui-icon-carat-1-sw { background-position: -80px 0; }
+.ui-icon-carat-1-w { background-position: -96px 0; }
+.ui-icon-carat-1-nw { background-position: -112px 0; }
+.ui-icon-carat-2-n-s { background-position: -128px 0; }
+.ui-icon-carat-2-e-w { background-position: -144px 0; }
+.ui-icon-triangle-1-n { background-position: 0 -16px; }
+.ui-icon-triangle-1-ne { background-position: -16px -16px; }
+.ui-icon-triangle-1-e { background-position: -32px -16px; }
+.ui-icon-triangle-1-se { background-position: -48px -16px; }
+.ui-icon-triangle-1-s { background-position: -64px -16px; }
+.ui-icon-triangle-1-sw { background-position: -80px -16px; }
+.ui-icon-triangle-1-w { background-position: -96px -16px; }
+.ui-icon-triangle-1-nw { background-position: -112px -16px; }
+.ui-icon-triangle-2-n-s { background-position: -128px -16px; }
+.ui-icon-triangle-2-e-w { background-position: -144px -16px; }
+.ui-icon-arrow-1-n { background-position: 0 -32px; }
+.ui-icon-arrow-1-ne { background-position: -16px -32px; }
+.ui-icon-arrow-1-e { background-position: -32px -32px; }
+.ui-icon-arrow-1-se { background-position: -48px -32px; }
+.ui-icon-arrow-1-s { background-position: -64px -32px; }
+.ui-icon-arrow-1-sw { background-position: -80px -32px; }
+.ui-icon-arrow-1-w { background-position: -96px -32px; }
+.ui-icon-arrow-1-nw { background-position: -112px -32px; }
+.ui-icon-arrow-2-n-s { background-position: -128px -32px; }
+.ui-icon-arrow-2-ne-sw { background-position: -144px -32px; }
+.ui-icon-arrow-2-e-w { background-position: -160px -32px; }
+.ui-icon-arrow-2-se-nw { background-position: -176px -32px; }
+.ui-icon-arrowstop-1-n { background-position: -192px -32px; }
+.ui-icon-arrowstop-1-e { background-position: -208px -32px; }
+.ui-icon-arrowstop-1-s { background-position: -224px -32px; }
+.ui-icon-arrowstop-1-w { background-position: -240px -32px; }
+.ui-icon-arrowthick-1-n { background-position: 0 -48px; }
+.ui-icon-arrowthick-1-ne { background-position: -16px -48px; }
+.ui-icon-arrowthick-1-e { background-position: -32px -48px; }
+.ui-icon-arrowthick-1-se { background-position: -48px -48px; }
+.ui-icon-arrowthick-1-s { background-position: -64px -48px; }
+.ui-icon-arrowthick-1-sw { background-position: -80px -48px; }
+.ui-icon-arrowthick-1-w { background-position: -96px -48px; }
+.ui-icon-arrowthick-1-nw { background-position: -112px -48px; }
+.ui-icon-arrowthick-2-n-s { background-position: -128px -48px; }
+.ui-icon-arrowthick-2-ne-sw { background-position: -144px -48px; }
+.ui-icon-arrowthick-2-e-w { background-position: -160px -48px; }
+.ui-icon-arrowthick-2-se-nw { background-position: -176px -48px; }
+.ui-icon-arrowthickstop-1-n { background-position: -192px -48px; }
+.ui-icon-arrowthickstop-1-e { background-position: -208px -48px; }
+.ui-icon-arrowthickstop-1-s { background-position: -224px -48px; }
+.ui-icon-arrowthickstop-1-w { background-position: -240px -48px; }
+.ui-icon-arrowreturnthick-1-w { background-position: 0 -64px; }
+.ui-icon-arrowreturnthick-1-n { background-position: -16px -64px; }
+.ui-icon-arrowreturnthick-1-e { background-position: -32px -64px; }
+.ui-icon-arrowreturnthick-1-s { background-position: -48px -64px; }
+.ui-icon-arrowreturn-1-w { background-position: -64px -64px; }
+.ui-icon-arrowreturn-1-n { background-position: -80px -64px; }
+.ui-icon-arrowreturn-1-e { background-position: -96px -64px; }
+.ui-icon-arrowreturn-1-s { background-position: -112px -64px; }
+.ui-icon-arrowrefresh-1-w { background-position: -128px -64px; }
+.ui-icon-arrowrefresh-1-n { background-position: -144px -64px; }
+.ui-icon-arrowrefresh-1-e { background-position: -160px -64px; }
+.ui-icon-arrowrefresh-1-s { background-position: -176px -64px; }
+.ui-icon-arrow-4 { background-position: 0 -80px; }
+.ui-icon-arrow-4-diag { background-position: -16px -80px; }
+.ui-icon-extlink { background-position: -32px -80px; }
+.ui-icon-newwin { background-position: -48px -80px; }
+.ui-icon-refresh { background-position: -64px -80px; }
+.ui-icon-shuffle { background-position: -80px -80px; }
+.ui-icon-transfer-e-w { background-position: -96px -80px; }
+.ui-icon-transferthick-e-w { background-position: -112px -80px; }
+.ui-icon-folder-collapsed { background-position: 0 -96px; }
+.ui-icon-folder-open { background-position: -16px -96px; }
+.ui-icon-document { background-position: -32px -96px; }
+.ui-icon-document-b { background-position: -48px -96px; }
+.ui-icon-note { background-position: -64px -96px; }
+.ui-icon-mail-closed { background-position: -80px -96px; }
+.ui-icon-mail-open { background-position: -96px -96px; }
+.ui-icon-suitcase { background-position: -112px -96px; }
+.ui-icon-comment { background-position: -128px -96px; }
+.ui-icon-person { background-position: -144px -96px; }
+.ui-icon-print { background-position: -160px -96px; }
+.ui-icon-trash { background-position: -176px -96px; }
+.ui-icon-locked { background-position: -192px -96px; }
+.ui-icon-unlocked { background-position: -208px -96px; }
+.ui-icon-bookmark { background-position: -224px -96px; }
+.ui-icon-tag { background-position: -240px -96px; }
+.ui-icon-home { background-position: 0 -112px; }
+.ui-icon-flag { background-position: -16px -112px; }
+.ui-icon-calendar { background-position: -32px -112px; }
+.ui-icon-cart { background-position: -48px -112px; }
+.ui-icon-pencil { background-position: -64px -112px; }
+.ui-icon-clock { background-position: -80px -112px; }
+.ui-icon-disk { background-position: -96px -112px; }
+.ui-icon-calculator { background-position: -112px -112px; }
+.ui-icon-zoomin { background-position: -128px -112px; }
+.ui-icon-zoomout { background-position: -144px -112px; }
+.ui-icon-search { background-position: -160px -112px; }
+.ui-icon-wrench { background-position: -176px -112px; }
+.ui-icon-gear { background-position: -192px -112px; }
+.ui-icon-heart { background-position: -208px -112px; }
+.ui-icon-star { background-position: -224px -112px; }
+.ui-icon-link { background-position: -240px -112px; }
+.ui-icon-cancel { background-position: 0 -128px; }
+.ui-icon-plus { background-position: -16px -128px; }
+.ui-icon-plusthick { background-position: -32px -128px; }
+.ui-icon-minus { background-position: -48px -128px; }
+.ui-icon-minusthick { background-position: -64px -128px; }
+.ui-icon-close { background-position: -80px -128px; }
+.ui-icon-closethick { background-position: -96px -128px; }
+.ui-icon-key { background-position: -112px -128px; }
+.ui-icon-lightbulb { background-position: -128px -128px; }
+.ui-icon-scissors { background-position: -144px -128px; }
+.ui-icon-clipboard { background-position: -160px -128px; }
+.ui-icon-copy { background-position: -176px -128px; }
+.ui-icon-contact { background-position: -192px -128px; }
+.ui-icon-image { background-position: -208px -128px; }
+.ui-icon-video { background-position: -224px -128px; }
+.ui-icon-script { background-position: -240px -128px; }
+.ui-icon-alert { background-position: 0 -144px; }
+.ui-icon-info { background-position: -16px -144px; }
+.ui-icon-notice { background-position: -32px -144px; }
+.ui-icon-help { background-position: -48px -144px; }
+.ui-icon-check { background-position: -64px -144px; }
+.ui-icon-bullet { background-position: -80px -144px; }
+.ui-icon-radio-off { background-position: -96px -144px; }
+.ui-icon-radio-on { background-position: -112px -144px; }
+.ui-icon-pin-w { background-position: -128px -144px; }
+.ui-icon-pin-s { background-position: -144px -144px; }
+.ui-icon-play { background-position: 0 -160px; }
+.ui-icon-pause { background-position: -16px -160px; }
+.ui-icon-seek-next { background-position: -32px -160px; }
+.ui-icon-seek-prev { background-position: -48px -160px; }
+.ui-icon-seek-end { background-position: -64px -160px; }
+.ui-icon-seek-start { background-position: -80px -160px; }
+/* ui-icon-seek-first is deprecated, use ui-icon-seek-start instead */
+.ui-icon-seek-first { background-position: -80px -160px; }
+.ui-icon-stop { background-position: -96px -160px; }
+.ui-icon-eject { background-position: -112px -160px; }
+.ui-icon-volume-off { background-position: -128px -160px; }
+.ui-icon-volume-on { background-position: -144px -160px; }
+.ui-icon-power { background-position: 0 -176px; }
+.ui-icon-signal-diag { background-position: -16px -176px; }
+.ui-icon-signal { background-position: -32px -176px; }
+.ui-icon-battery-0 { background-position: -48px -176px; }
+.ui-icon-battery-1 { background-position: -64px -176px; }
+.ui-icon-battery-2 { background-position: -80px -176px; }
+.ui-icon-battery-3 { background-position: -96px -176px; }
+.ui-icon-circle-plus { background-position: 0 -192px; }
+.ui-icon-circle-minus { background-position: -16px -192px; }
+.ui-icon-circle-close { background-position: -32px -192px; }
+.ui-icon-circle-triangle-e { background-position: -48px -192px; }
+.ui-icon-circle-triangle-s { background-position: -64px -192px; }
+.ui-icon-circle-triangle-w { background-position: -80px -192px; }
+.ui-icon-circle-triangle-n { background-position: -96px -192px; }
+.ui-icon-circle-arrow-e { background-position: -112px -192px; }
+.ui-icon-circle-arrow-s { background-position: -128px -192px; }
+.ui-icon-circle-arrow-w { background-position: -144px -192px; }
+.ui-icon-circle-arrow-n { background-position: -160px -192px; }
+.ui-icon-circle-zoomin { background-position: -176px -192px; }
+.ui-icon-circle-zoomout { background-position: -192px -192px; }
+.ui-icon-circle-check { background-position: -208px -192px; }
+.ui-icon-circlesmall-plus { background-position: 0 -208px; }
+.ui-icon-circlesmall-minus { background-position: -16px -208px; }
+.ui-icon-circlesmall-close { background-position: -32px -208px; }
+.ui-icon-squaresmall-plus { background-position: -48px -208px; }
+.ui-icon-squaresmall-minus { background-position: -64px -208px; }
+.ui-icon-squaresmall-close { background-position: -80px -208px; }
+.ui-icon-grip-dotted-vertical { background-position: 0 -224px; }
+.ui-icon-grip-dotted-horizontal { background-position: -16px -224px; }
+.ui-icon-grip-solid-vertical { background-position: -32px -224px; }
+.ui-icon-grip-solid-horizontal { background-position: -48px -224px; }
+.ui-icon-gripsmall-diagonal-se { background-position: -64px -224px; }
+.ui-icon-grip-diagonal-se { background-position: -80px -224px; }
+
+
+/* Misc visuals
+----------------------------------*/
+
+/* Corner radius */
+.ui-corner-tl { -moz-border-radius-topleft: 5px; -webkit-border-top-left-radius: 5px; border-top-left-radius: 5px; }
+.ui-corner-tr { -moz-border-radius-topright: 5px; -webkit-border-top-right-radius: 5px; border-top-right-radius: 5px; }
+.ui-corner-bl { -moz-border-radius-bottomleft: 5px; -webkit-border-bottom-left-radius: 5px; border-bottom-left-radius: 5px; }
+.ui-corner-br { -moz-border-radius-bottomright: 5px; -webkit-border-bottom-right-radius: 5px; border-bottom-right-radius: 5px; }
+.ui-corner-top { -moz-border-radius-topleft: 5px; -webkit-border-top-left-radius: 5px; border-top-left-radius: 5px; -moz-border-radius-topright: 5px; -webkit-border-top-right-radius: 5px; border-top-right-radius: 5px; }
+.ui-corner-bottom { -moz-border-radius-bottomleft: 5px; -webkit-border-bottom-left-radius: 5px; border-bottom-left-radius: 5px; -moz-border-radius-bottomright: 5px; -webkit-border-bottom-right-radius: 5px; border-bottom-right-radius: 5px; }
+.ui-corner-right { -moz-border-radius-topright: 5px; -webkit-border-top-right-radius: 5px; border-top-right-radius: 5px; -moz-border-radius-bottomright: 5px; -webkit-border-bottom-right-radius: 5px; border-bottom-right-radius: 5px; }
+.ui-corner-left { -moz-border-radius-topleft: 5px; -webkit-border-top-left-radius: 5px; border-top-left-radius: 5px; -moz-border-radius-bottomleft: 5px; -webkit-border-bottom-left-radius: 5px; border-bottom-left-radius: 5px; }
+.ui-corner-all { -moz-border-radius: 5px; -webkit-border-radius: 5px; border-radius: 5px; }
+
+/* Overlays */
+.ui-widget-overlay { background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .30;filter:Alpha(Opacity=30); }
+.ui-widget-shadow { margin: -8px 0 0 -8px; padding: 8px; background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .30;filter:Alpha(Opacity=30); -moz-border-radius: 8px; -webkit-border-radius: 8px; border-radius: 8px; }/*
+ * jQuery UI Progressbar 1.8.9
+ *
+ * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * http://docs.jquery.com/UI/Progressbar#theming
+ */
+.ui-progressbar { height:20px; text-align: left; }
+.ui-progressbar .ui-progressbar-value {margin: -1px; height:20px; } \ No newline at end of file
diff --git a/views/about.haml b/views/about.haml
deleted file mode 100644
index da0f836..0000000
--- a/views/about.haml
+++ /dev/null
@@ -1,4 +0,0 @@
-%p
- A demonstration application for the
- %a{:href => "http://www.opentox.org"} OpenTox
- framework.
diff --git a/views/classification_validation.haml b/views/classification_validation.haml
index 94ba8f9..41362ba 100644
--- a/views/classification_validation.haml
+++ b/views/classification_validation.haml
@@ -1,17 +1,17 @@
%dt Correct predictions:
%dd
- = sprintf("%.2f", model.correct_predictions) if model.correct_predictions
+ = sprintf("%.2f", model.correct_predictions.to_f) if model.correct_predictions
= '%'
%dt
%a{:href => "http://en.wikipedia.org/wiki/Receiver_operating_characteristic", :target => "_blank"} Weighted area under ROC:
%dd
- = sprintf("%.3f", model.weighted_area_under_roc) if model.weighted_area_under_roc
+ = sprintf("%.3f", model.weighted_area_under_roc.to_f) if model.weighted_area_under_roc
%dt
%a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Specificity:
-%dd= sprintf("%.3f", model.specificity) if model.specificity
+%dd= sprintf("%.3f", model.specificity.to_f) if model.specificity
%dt
%a{:href => "http://en.wikipedia.org/wiki/Sensitivity_and_specificity", :target => "_blank"} Sensitivity:
-%dd= sprintf("%.3f", model.sensitivity) if model.sensitivity
+%dd= sprintf("%.3f", model.sensitivity.to_f) if model.sensitivity
%dt
%a{:href => "http://en.wikipedia.org/wiki/Confusion_matrix", :target => "_blank"} Confusion Matrix:
%dd
diff --git a/views/compound_image.haml b/views/compound_image.haml
index c6f962a..18944dc 100644
--- a/views/compound_image.haml
+++ b/views/compound_image.haml
@@ -1,2 +1,2 @@
-%img{:src => compound.display_smarts_uri(features[:activating].collect{|f| f[:smarts]},@features[:deactivating].collect{|f| f[:smarts]}), :alt => compound.smiles}
+%img{:src => compound.matching_smarts_image_uri(features[:activating].collect{|f| f[:smarts]},features[:deactivating].collect{|f| f[:smarts]}), :alt => compound.to_smiles}
diff --git a/views/create.haml b/views/create.haml
index 20de401..c04f841 100644
--- a/views/create.haml
+++ b/views/create.haml
@@ -18,13 +18,11 @@
= link_to "instructions for creating training datasets", '/help'
before submitting.
- %form{ :action => url_for('/upload'), :method => "post", :enctype => "multipart/form-data" }
+ %form{ :action => url_for('/models'), :method => "post", :enctype => "multipart/form-data" }
+ %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
%fieldset
- %label{:for => 'endpoint'} 1. Enter #{toggle_link("#endpoint_description","endpoint")} name and #{toggle_link("#unit","unit")} (for #{toggle_link("#regression","regression")}):
- %input{:type => 'text', :name => 'endpoint', :id => 'endpoint', :size => '50'}
- %br
%label{:for => 'file'}
- 2. Upload training data in
+ Select training data in
= link_to "Excel", '/help'
or
= link_to "CSV", '/help'
@@ -39,3 +37,14 @@
= haml :regression, :layout => false
= haml :endpoint, :layout => false
= haml :unit, :layout => false
+
+ .login_notice
+
+ - if session[:username] == "guest"
+ You are currently logged in as
+ %b guest
+ and your models can be modified or deleted by other guests. Please
+ = link_to "log in", "/login"
+ with your
+ %a{:href => "www.opentox.org"} OpenTox
+ account to control your model permissions.
diff --git a/views/delete.haml b/views/delete.haml
deleted file mode 100644
index 88457e0..0000000
--- a/views/delete.haml
+++ /dev/null
@@ -1,25 +0,0 @@
-%hr
-%p
- You are going to remove the
- = @model['name']
- model permanently!
-%p Enter your username/password if you are sure or cancel the operation.
-
-%form{ :action => "/#{params[:id]}", :method => "post" }
- %input{:type => 'hidden', :name => "_method", :value => "delete"}
-
- %table
- %tr
- %th Username:
- %td
- %input{:type => "text", :name => "username"}
- %tr
- %th Password:
- %td
- %input{:type => "text", :name => "password"}
-
- %tr
- %td
- %input{:type => "submit", :value => "Delete"}
- %td
- %a{:href => '/'} Cancel
diff --git a/views/features.haml b/views/features.haml
deleted file mode 100644
index 55f53f3..0000000
--- a/views/features.haml
+++ /dev/null
@@ -1,13 +0,0 @@
-%a{:href => "create"}Select/create dataset
-&rarr; Select endpoint
-%p Dataset #{@dataset_uri} contains more than one endpoint.
-%p Please select an endpoint to predict:
-%form{ :action => 'create', :method => "post" }
- %input{:type => :hidden, :name => :dataset_uri, :value => @dataset_uri}
- %p
- %select{:name => "feature_uri"}
- - @features.each do |uri,title|
- %option{:value => uri} #{title}
- %input{ :type => "submit", :value => "Select"}
- %a{:href => 'create'} Cancel
-
diff --git a/views/fragment.haml b/views/fragment.haml
index fa7495d..3b9f68b 100644
--- a/views/fragment.haml
+++ b/views/fragment.haml
@@ -2,6 +2,7 @@
%input{:type => :hidden, :name => :compound_uri, :value => compound_uri}
%input{:type => :hidden, :name => :model_uri, :value => model_uri}
%input{:type => :hidden, :name => :highlight, :value => smarts}
+ %input{:type => :hidden, :name => :subjectid, :value => session[:subjectid]}
- if smarts.nil?
%input{ :type => "submit", :value => "Reset"}
- else
diff --git a/views/help.haml b/views/help.haml
index eabf978..a8bbf4b 100644
--- a/views/help.haml
+++ b/views/help.haml
@@ -20,7 +20,7 @@
Input files are accepted in
%a{:href => "http://en.wikipedia.org/wiki/Microsoft_Excel"} Excel
and
- %a{:href => "en.wikipedia.org/wiki/Comma-separated_values"} CSV
+ %a{:href => "http://en.wikipedia.org/wiki/Comma-separated_values"} CSV
formats.
%h3 Excel example
diff --git a/views/layout.haml b/views/layout.haml
index a3db5e9..d54b413 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -6,12 +6,15 @@
%title ToxCreate
%script{:type => "text/javascript", :src => "javascripts/jquery.js"}
%script{:type => "text/javascript", :src => "javascripts/toxcreate.js"}
- %link{:rel=>'stylesheet', :href=>'stylesheets/style.css', :type => "text/css"}
+ %script{:type => "text/javascript", :src => "javascripts/jquery-ui-progressbar.js"}
+ %link{:rel=>'stylesheet', :href=>'stylesheets/style.css', :type => "text/css"}
+ %link{:rel=>'stylesheet', :href=>'progressbar/progressbar.css', :type => "text/css"}
%body
.logo
= image_tag "/ToxCreate_rgb_72.png", :alt => 'ToxCreate', :align => 'right'
- %br Create and evaluate models to predict toxicity
+ %br
+ Create and evaluate models to predict toxicity
.index
%ul
%li{:class => ("selected" if /\/create/ =~ request.path )}
@@ -20,10 +23,17 @@
= link_to "Inspect", "/models"
%li{:class => ("selected" if /predict|lazar/ =~ request.path )}
= link_to "Predict", "/predict"
+ - if AA_SERVER
+ %li{:class => ("selected" if /login/ =~ request.path )}
+ = link_to "Login", "/login"
%li{:class => ("selected" if /help/ =~ request.path )}
= link_to "Help", "/help"
.content
+ .login_info
+ User:
+ %b= session[:username]
+
- if `hostname`.match(/ot-test/)
.notice
This service is for testing purposes only - once a week all models will be deleted. Please send bug reports and feature requests to our
diff --git a/views/lazar.haml b/views/lazar.haml
index 59d5396..3de7400 100644
--- a/views/lazar.haml
+++ b/views/lazar.haml
@@ -1,55 +1,59 @@
-%p= link_to "New prediction", "/predict"
-.lazar-predictions
-
- -# explanations
- = haml :lazar_algorithm, :layout => false
- = haml :confidence, :layout => false
- = haml :similarity, :layout => false
- = haml :significant_fragments, :layout => false
- = haml :training_data, :layout => false
-
- %a{:name => "prediction"}
- %table
- %thead
- %tr
- %th= @title.gsub(/_lazar_.*$/,' ').capitalize
- %th= toggle_link("#lazar_algorithm","Prediction")
- %th= toggle_link("#confidence","Confidence")
- %th Supporting information
-
- %tr
- %td.image= compound_image(@compound,@features)
- %td= activity_markup(@activity)
- %td= sprintf('%.03g', @confidence.to_f.abs) if @confidence
- %td
- %ul
- %li
- %a{:href => "#prediction", :id => "show_names"} Names and synonyms
- :javascript
- $("a#show_names").click(function () {
- $("#compound_names").load("#{File.join("compound",@compound.inchi)}");
- $("tr#names").toggle();
- });
- %li= toggle_link("#fragments","Significant fragments")
- -# This does not work, ask nina/vedrin
- -# %li
- %a{:href => "http://ambit.uni-plovdiv.bg:8080/ambit2/query/structure/?search=#{@compound.smiles}"} Ambit data
- -# %li
- %a{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pccompound&term=#{URI.encode('"'+@compound.inchi+'"[InChI]')}"} PubChem data
- (external)
- -# %li
- %a{:href => "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&inchi=#{URI.encode @compound.inchi}"} ToxNet data
- -#http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&regno=000143157
-
- %tr#names{ :style => "display: none;" }
- %td{:colspan => '4'}
- %a{:name => 'names'}
- = hide_link('#names')
- #compound_names
- %tr#fragments{ :style => "display: none;" }
- %td{:colspan => '4'}
- = hide_link('#fragments')
- = haml :feature_table, :locals => {:features => @features}, :layout => false
-
- %tbody#neighbors
- = haml :neighbors, :locals => {:neighbors => @neighbors, :page => @page}, :layout => :false
+%p= link_to "New prediction", "/predict"
+.lazar-predictions
+
+ -# explanations
+ = haml :lazar_algorithm, :layout => false
+ = haml :confidence, :layout => false
+ = haml :similarity, :layout => false
+ = haml :significant_fragments, :layout => false
+ = haml :training_data, :layout => false
+
+ %a{:name => "prediction"}
+ %table
+ %thead
+ %tr
+ %th= @prediction.title
+ %th= toggle_link("#lazar_algorithm","Prediction")
+ %th= toggle_link("#confidence","Confidence")
+ %th Supporting information
+
+ %tr
+ -# %td
+ %img{:src => @compound.to_image_uri, :alt => @compound.to_smiles}
+ %td.image= compound_image(@compound,@prediction.descriptors(@compound))
+ %td= activity_markup(@prediction.value(@compound))
+ %td= sprintf('%.03g', @prediction.confidence(@compound))
+ -#%td= @prediction.confidence(@compound)
+ %td
+ %ul
+ %li
+ %a{:href => "#prediction", :id => "show_names"} Names and synonyms
+ :javascript
+ $("a#show_names").click(function () {
+ $("#compound_names").load("#{File.join("/compound",@compound.inchi)}");
+ $("tr#names").toggle();
+ });
+ %li= toggle_link("#fragments","Significant fragments")
+ -# This does not work, ask nina/vedrin
+ -# %li
+ %a{:href => "http://ambit.uni-plovdiv.bg:8080/ambit2/query/structure/?search=#{@compound.smiles}"} Ambit data
+ -# %li
+ %a{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=PureSearch&db=pccompound&term=#{URI.encode('"'+@compound.inchi+'"[InChI]')}"} PubChem data
+ (external)
+ -# %li
+ %a{:href => "http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&inchi=#{URI.encode @compound.inchi}"} ToxNet data
+ -#http://chem.sis.nlm.nih.gov/chemidplus/direct.jsp?result=advanced&regno=000143157
+
+ %tr#names{ :style => "display: none;" }
+ %td{:colspan => '4'}
+ %a{:name => 'names'}
+ = hide_link('#names')
+ #compound_names
+ %tr#fragments{ :style => "display: none;" }
+ %td{:colspan => '4'}
+ = hide_link('#fragments')
+ = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(@compound))}, :layout => false
+
+ %tbody#neighbors
+ = haml :neighbors, :locals => {:neighbors => @prediction.neighbors(@compound), :page => @page}, :layout => false
+
diff --git a/views/login.haml b/views/login.haml
new file mode 100644
index 0000000..6d15bb7
--- /dev/null
+++ b/views/login.haml
@@ -0,0 +1,47 @@
+.input
+
+ - if session[:username] == "guest"
+ .login_notice
+ You are currently logged in as
+ %b guest
+ and your models can be modified or deleted by other guests.
+ To control models permissions you can
+ log in with your
+ %a{:href => "http://www.opentox.org"} OpenTox
+ username/password below. If have no
+ %a{:href => "http://www.opentox.org"} OpenTox
+ account yet you can
+ %a{:href => "http://www.opentox.org/join_form"} register here.
+ - else
+ %p
+ Change
+ %a{:href => "http://www.opentox.org"} OpenTox
+ account:
+
+ -# if !logged_in()
+ %form{ :action => url_for('/login'), :method => "post" }
+ %fieldset
+ %label{:for => 'username'} Username:
+ %input{:type => 'text', :name => 'username', :id => 'username', :size => '50'}
+ %br
+ %label{:for => 'password'} Password:
+ %input{:type => 'password', :name => 'password', :id => 'password', :size => '50'}
+ %input{ :type => "submit", :value => "Login"}
+ = link_to "Cancel", '/login'
+ - if session[:username] != "guest"
+ %br
+ %form{ :action => url_for('/login'), :method => "post" }
+ %input{:type => 'hidden', :name => 'username', :id => 'username', :value => "guest"}
+ %input{:type => 'hidden', :name => 'password', :id => 'password', :value => "guest"}
+ %input{ :type => "submit", :value => "Login as guest"}
+ -# else
+ %form{ :action => url_for('/logout'), :method => "post" }
+ -#%p
+ You are logged in as:
+ %b= session[:username]
+ -# if LOGGER.level == Logger::DEBUG
+ %br
+ = session[:subjectid]
+ %input{ :type => "submit", :value => "Switch user"}
+ = link_to "Cancel", '/login'
+
diff --git a/views/model.haml b/views/model.haml
index 454423a..e1bdd99 100644
--- a/views/model.haml
+++ b/views/model.haml
@@ -1,61 +1,85 @@
- uri = url_for("/model/#{model.id}", :full)
-- js = "$('#delete_#{model.id}').deleteModel('DELETE', {elem: '#model_#{model.id}'});\n " + "$('#show_model_#{model.id}_warnings').toggleWarnings('#{model.id}');"
+- js = "$('#delete_#{model.id}').deleteModel('DELETE', {id: '#{model.id}'});\n " + "$('#show_model_#{model.id}_warnings').toggleWarnings('#{model.id}');\n"
:javascript
$(function() {
#{js}
});
-%div{:id => "model_#{model.id}"}
- %h2
- = model.name
-
+%div{:id => "model_#{model.id}"}
+ %div{:id => "model_#{model.id}_name"}
+ = haml :model_name, :locals=>{:model=>model}, :layout => false
.model
%dl
%dt Status:
%dd
- %span{:id => "model_#{model.id}_status", :class => model.status}
- = haml :model_status, :locals=>{:model=>model}, :layout => false
- (
- %a{:href => url_for("/model/#{model.id}"), :id => "delete_#{model.id}", :class => 'delete'} delete
- )
- %dt Started:
- %dd= model.created_at.strftime("%m/%d/%Y - %I:%M:%S%p")
- %dt Training compounds:
- %dd= model.nr_compounds
- %dt Warnings:
- - if model.warnings == ''
- %dd -
- - else
+ %span{:id => "model_#{model.id}_status", :class => "model_status"}
+ = haml :model_status, :locals=>{:model=>model}, :layout => false
+ - if model.task_uri && model.status !~ /Completed|Cancelled|Error|Deleting/
+ - if (task = OpenTox::Task.exist?(model.task_uri))
+ %input{:type => 'hidden', :id => "model_#{model.id}_task", :value => "#{model.task_uri}"}
+ - percentage_completed = task.metadata[OT.percentageCompleted].to_i
+ - js = "$('#model_#{model.id}_progress').progressbar({ value: #{percentage_completed} })";
+ :javascript
+ $(function() {
+ #{js}
+ });
+
+ %div{:id => "model_#{model.id}_progress", :class => "model_progress", :title => "#{percentage_completed}%", :alt => "#{percentage_completed}%"}
+ //= haml :model_progress, :locals=>{:percentage_completed=>percentage_completed}, :layout => false
+ - if is_authorized(model.web_uri, "DELETE")
+ %a{:href => url_for("/model/#{model.id}"), :id => "delete_#{model.id}", :class => 'delete_link'}
+ - if model.status == "Completed"
+ (delete)
+ - else
+ (stop)
+ %span
+ %br
+
+ -#%dt Started:
+ -#%dd= model.created_at.strftime("%m/%d/%Y - %I:%M:%S%p")
+ - if model.nr_compounds
+ %dt Training compounds:
+ %dd= model.nr_compounds
+ - if model.error_messages
+ %dt Errors:
+ %dd= model.error_messages
+ - if model.warnings
+ %dt Warnings:
%a{:href => "#", :id => "show_model_#{model.id}_warnings"} show
%dd{:id => "model_#{model.id}_warnings", :style => "display: none;"}= model.warnings
-
- - if model.status == 'Completed'
- %dt Algorithm:
- %dd
- = toggle_link("#lazar_description","lazar")
+ %dt Algorithm:
+ %dd= toggle_link("#lazar_description","lazar")
+ - if model.type
%dt Type:
%dd= toggle_link("##{model.type}","#{model.type}")
- %dt Descriptors:
- %dd
- %a{:href => 'http://www.maunz.de/libfminer2-bbrc-doc/'} Fminer backbone refinement classes
+ %dt Descriptors:
+ %dd
+ %a{:href => 'http://www.maunz.de/libfminer2-bbrc-doc/'} Fminer backbone refinement classes
+ - if model.training_dataset
%dt Training dataset:
%dd
- %a{:href => "#{model.training_dataset}.xls"} Excel sheet
+ %a{:href => "#{model.training_dataset}.xls#{subjectstring}"} Excel sheet
,
- %a{:href => "#{model.training_dataset}.rdf"} RDF/XML
- %em (experts) ,
- %a{:href => "#{model.training_dataset}.yaml"} YAML
+ -#%a{:href => "#{model.training_dataset}.rdf"} RDF/XML
+ -#%em (experts) ,
+ %a{:href => "#{model.training_dataset}.yaml#{subjectstring}" } YAML
%em (experts)
+ - if model.feature_dataset
%dt Feature dataset:
%dd
- %a{:href => "#{model.feature_dataset}.rdf"} RDF/XML
+ -#%a{:href => "#{model.feature_dataset}.rdf"} RDF/XML
+ -#,
+ %a{:href => "#{model.feature_dataset}.xls#{subjectstring}"} Excel sheet
,
- %a{:href => "#{model.feature_dataset}.yaml"} YAML
- %em (experts, dataset too large for Excel)
+ %a{:href => "#{model.feature_dataset}.yaml#{subjectstring}"} YAML
+ %em (experts)
+ - if model.uri
%dt Model:
%dd
- %a{:href => "#{model.uri}.rdf"} RDF/XML
- ,
- %a{:href => "#{model.uri}.yaml"} YAML
+ -#%a{:href => "#{model.uri}.rdf"} RDF/XML
+ -#,
+ - if model.validation_qmrf_uri
+ %a{:href => File.join(model.validation_qmrf_uri,"editor")} QMRF Editor,
+ %a{:href => "#{model.uri}.yaml#{subjectstring}"} YAML
%em (experts, models cannot be represented in Excel)
- = haml :validation, :locals=>{:model=>model}, :layout => false
+ = haml :validation, :locals=>{:model=>model,:subjectstring => subjectstring}, :layout => false
diff --git a/views/model_name.haml b/views/model_name.haml
new file mode 100644
index 0000000..b1f6f10
--- /dev/null
+++ b/views/model_name.haml
@@ -0,0 +1,12 @@
+- js = "$('#edit_#{model.id}').editModel('PUT', {id: '#{model.id}', mode: 'edit'});\n "
+:javascript
+ $(function() {
+ #{js}
+ });
+%h2
+ = model.name
+ - if is_authorized(model.web_uri, "PUT")
+ %span{:class => "edit_button"}
+ (
+ %a{:href => url_for("/model/#{model.id}/name?mode=edit"), :id => "edit_#{model.id}"} edit
+ ) \ No newline at end of file
diff --git a/views/model_name_edit.haml b/views/model_name_edit.haml
new file mode 100644
index 0000000..aec59fc
--- /dev/null
+++ b/views/model_name_edit.haml
@@ -0,0 +1,14 @@
+- js = "$('#cancel_#{model.id}').editModel('GET', {id: '#{model.id}', mode: 'show'});\n "
+- js = "$('#save_#{model.id}').saveModel('POST', {id: '#{model.id}', mode: 'show'});\n "
+:javascript
+ $(function() {
+ #{js}
+ });
+%form{:name => "form", :action => url_for("/model/#{model.id}"), :method => "post", :enctype => "multipart/form-data" }
+ %input{:type => 'text', :name => 'name', :id => "model_#{model.id}_name", :class => 'input_model_name', :size => '40', :value => model.name}
+ %input{:type => 'hidden', :name => 'id', :id => 'id', :value => model.id}
+ %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
+ %input{ :type => "submit", :value => "Save", :id => "save_#{model.id}", :class => "edit_button"}
+ %span{:class => "edit_button"}
+ %a{:href => url_for("/model/#{model.id}/name?mode=show"), :id => "cancel_#{model.id}"} Cancel
+
diff --git a/views/model_progress.haml b/views/model_progress.haml
new file mode 100644
index 0000000..0064ae1
--- /dev/null
+++ b/views/model_progress.haml
@@ -0,0 +1 @@
+= percentage_completed
diff --git a/views/model_status.haml b/views/model_status.haml
index 1357d99..60e1eaf 100644
--- a/views/model_status.haml
+++ b/views/model_status.haml
@@ -1,2 +1 @@
-= image_tag("/snake_transparent.gif") if model.status.match(/running|started|created/i)
-= model.status
+= model.status.to_s
diff --git a/views/models.haml b/views/models.haml
index 6712e3d..a99144a 100644
--- a/views/models.haml
+++ b/views/models.haml
@@ -1,15 +1,16 @@
-- stati = @models.map{|m| "#{m.id}" if m.status != "Completed"}.compact
+- stati = @models.map{|m| "#{m.id}" if m.status !~ /Completed|Error/}.compact
- stati_to_check = stati.length > 0 ? stati.join(", ") : stati = 0
:javascript
$(function() {
if(#{stati != 0}) {
- setTimeout('checkStati("#{stati_to_check}")',1500);
+ setTimeout('checkStati("#{stati_to_check}", "#{subjectstring}")',5000);
}
var reload_validation = true;
- if(reload_validation) setTimeout('checkValidation()',15000);
+ //if(reload_validation) setTimeout('checkValidation()',15000);
});
-%p Get an overview about ToxCreate models. This page is refreshed every 15 seconds to update the model status.
+-# %p Get an overview about ToxCreate models. This page is refreshed every 15 seconds to update the model status.
+%p Get an overview about ToxCreate models. This page is refreshed every 5 seconds to update the model status.
-# explanations
= haml :lazar_description, :layout => false
@@ -17,4 +18,4 @@
= haml :regression, :layout => false
- @models.each do |model|
- = haml :model, :locals=>{:model=>model}, :layout => false
+ = haml :model, :locals=>{:model=>model,:subjectstring=>subjectstring}, :layout => false
diff --git a/views/neighbors.haml b/views/neighbors.haml
index 82fafd2..87fef13 100644
--- a/views/neighbors.haml
+++ b/views/neighbors.haml
@@ -9,15 +9,14 @@
- first = 5*page
- last = first+4
- neighbor_id = 0
-- neighbors.sort{|a,b| b.last[:similarity] <=> a.last[:similarity]}[first..last].each do |uri,data|
+-# LOGGER.debug neighbors.to_yaml
+- neighbors.sort{|a,b| b[OT.similarity] <=> a[OT.similarity]}[first..last].each do |neighbor|
- neighbor_id += 1
- - compound = OpenTox::Compound.new(:uri => uri)
+ - compound = OpenTox::Compound.new(neighbor[OT.compound])
%tr
- %td.image= compound_image(compound,data[:features])
- %td
- - data[:activities].each do |act|
- = activity_markup(act)
- %td= sprintf('%.03g', data[:similarity])
+ %td.image= compound_image(compound,@prediction.descriptors(compound))
+ %td= activity_markup(neighbor[OT.activity])
+ %td= sprintf('%.03g', neighbor[OT.similarity])
%td
%ul
%li
@@ -41,5 +40,5 @@
%tr{:id => "fragments#{neighbor_id}", :style => "display: none;" }
%td{:colspan => '4'}
= hide_link("#fragments#{neighbor_id}")
- = haml :feature_table, :locals => {:features => data[:features]}, :layout => false
+ = haml :feature_table, :locals => {:features => sort(@prediction.descriptors(compound))}, :layout => false
diff --git a/views/neighbors_navigation.haml b/views/neighbors_navigation.haml
index 43ec3ed..bf5ebb3 100644
--- a/views/neighbors_navigation.haml
+++ b/views/neighbors_navigation.haml
@@ -3,13 +3,14 @@
%form{:name => "nav", :action => url_for('/lazar#prediction'), :method => "post", :enctype => "multipart/form-data", :id => "nav"}
%input{:type => :hidden, :name => :compound_uri, :value => @compound.uri}
%input{:type => :hidden, :name => :model_uri, :value => @model_uri}
+ %input{:type => :hidden, :name => :subjectid, :value => session[:subjectid]}
%input{:type => :hidden, :name => :page, :id => "page"}
#prev= "prev" unless @page.to_i == 0
- = "(#{5*@page+1}-#{5*@page+5}/#{@neighbors.size})"
+ = "(#{5*@page+1}-#{5*@page+5}/#{@prediction.neighbors(@compound).size})"
- #next= "next" unless 5*@page.to_i+5 >= @neighbors.size
+ #next= "next" unless 5*@page.to_i+5 >= @prediction.neighbors(@compound).size
:javascript
$("#prev").click(function() {
diff --git a/views/predict.haml b/views/predict.haml
index 26c8094..347592c 100644
--- a/views/predict.haml
+++ b/views/predict.haml
@@ -26,9 +26,11 @@
- @models.each do |model|
%label{:for => model.id}
= model.name
- %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => model.id}
+ -#%input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => model.id, :disabled => !is_authorized(model.uri, "GET")}
+ %input{:type => 'checkbox', :name => "selection[#{model.id}]", :value => true, :id => model.id, :disabled => false}
%br
+ %input{:type => 'hidden', :name => 'subjectid', :id => 'subjectid', :value => session[:subjectid]}
%input{ :type => "submit", :value => "Predict", :onclick => "getsmiles();"}
= link_to 'Cancel', '/predict'
diff --git a/views/prediction.haml b/views/prediction.haml
index 0140b5e..9bb3f76 100644
--- a/views/prediction.haml
+++ b/views/prediction.haml
@@ -7,8 +7,9 @@
= @identifier
%tr
%td
- %img{:src => @compound.image_uri, :alt => @compound.smiles}
+ %img{:src => @compound.to_image_uri, :alt => @compound.to_smiles}
- @predictions.each do |p|
+ - LOGGER.debug p.to_yaml
%td
%b
= p[:title] + ":"
@@ -25,8 +26,8 @@
});
)
- - elsif p[:prediction].to_s.match(/not available/)
- = p[:prediction]
+ - elsif p[:error]
+ %br= p[:error]
- else
= activity_markup(p[:prediction])
- if p[:confidence]
@@ -43,6 +44,7 @@
%form{:name => "form", :action => url_for('/lazar'), :method => "post", :enctype => "multipart/form-data" }
%input{:type => :hidden, :name => :compound_uri, :value => @compound.uri}
%input{:type => :hidden, :name => :model_uri, :value => p[:model_uri]}
+ %input{:type => :hidden, :name => :subjectid, :value => session[:subjectid]}
%input{ :type => "submit", :value => "Details"}
= haml :confidence, :layout => false
diff --git a/views/style.sass b/views/style.sass
index ea9e65a..db1f1bf 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -4,7 +4,7 @@ $fg_color: #424345
$ot_purple: #5d308a
$body_color: white
$text_color: black
-$notice_border: black
+$notice_border: red
body
min-width: 30em
@@ -34,13 +34,10 @@ body
margin: 0
padding: 2px
display: inline
- border-right: 1px solid
- color: $body_color
- border-top: 1px solid
- color: $body_color
+ border-right: 1px solid $body_color
+ border-bottom: 1px solid $body_color
background-color: $fg_color
- padding-left: 0.5em
- padding-right: 0.5em
+ padding: 0.2em 0.5em
font-weight: bold
a
text-decoration: none
@@ -50,48 +47,55 @@ body
li.selected
font-weight: bold
background-color: $bg_color
- border: 1px solid
- color: $fg_color
- border-bottom: 1px solid
- color: $bg_color
+ border-bottom: 1px solid $bg_color
a
color: $text_color
.content
+ clear: both
background-color: $bg_color
height: 100%
padding: 1em
- border: 1px solid
- color: $fg_color
+ border-top: 1px solid $body_color
h2
margin: 20px 3px 2px 3px
.notice
- padding: 1em
+ //clear: both
+ //margin-top: 1em
+ padding: 0.5em 1em
background-color: $body_color
border: 1px solid
border-color: $notice_border
+ .login_info
+ text-align: right
+ font-size: small
+ .login_notice
+ //clear: both
+ font-size: small
+ background-color: $bg_color
+ padding: 1em 0em
+ //font-style: italic
.input
+ //clear: both
text-align: left
form
padding: 1em
background-color: $bg_color2
- border: 1px solid
- color: $fg_color
fieldset
- margin: 0
+ //margin: 0
padding: 0
+ padding-right: 1em
border: 0
legend
font-weight: bold
color: $fg_color
label
- width: 25em
- display: block
- float: left
+ //width: 28em
+ //display: block
+ //float: left
br
- clear: both
+ //clear: both
.code
- border: 1px solid black
padding: 1%
background-color: white
table
@@ -182,9 +186,9 @@ body
//overflow-y: scroll;
.model
- padding: 0em 1em
+ padding: 0.5em 1em
background-color: $bg_color2
- border: 1px solid
+ border: 0
margin-top: 0.6em
dl
dt
@@ -237,3 +241,22 @@ dl
padding: 0.3em
table
border-collapse: collapse
+.input_model_name
+ margin: 20px 3px 2px 3px
+ font-size: 1.2em
+ font-weight: bold
+ border: 0
+ background-color: #FEFEFF
+
+.edit_button
+ font-size: 0.5em
+
+.model_status
+ float: left
+
+.model_progress
+ width: 200px
+ height: 16px
+ margin-left: 16px
+ margin-right: 16px
+ float: left
diff --git a/views/validation.haml b/views/validation.haml
index bb44058..ce35536 100644
--- a/views/validation.haml
+++ b/views/validation.haml
@@ -1,18 +1,14 @@
-%dl{:id => "model_validation_#{model.id}"}
- %dt
- Validation:
- %input{ :id => "model_validation_report_#{model.id}", :type => "hidden", :value => "#{model.validation_report_status}", :class => "model_validation_report" }
- %dd
- - if model.validation_uri
+- if model.validation_uri
+ %dl{:id => "model_validation_#{model.id}"}
+ %dt
+ Validation:
+ -# %input{ :id => "model_validation_report_#{model.id}", :type => "hidden", :value => "#{model.validation_report_status}", :class => "model_validation_report" }
+ %dd
%dl
- %dt
- Detailed report:
- %dd
- - if model.validation_report_uri
- %a{:href => model.validation_report_uri, :target => "_blank"} show
- - else
- = image_tag("/snake_transparent.gif") if model.validation_report_status == "Running"
- %a{:href => model.validation_report_task_uri} #{model.validation_report_status}
+ - if model.validation_report_uri
+ %dt Detailed report:
+ %dd
+ %a{:href => model.validation_report_uri + subjectstring, :target => "_blank"} show
%dt Number of predictions
%dd= model.nr_predictions
- case model.type
@@ -20,8 +16,8 @@
= haml :classification_validation, :locals=>{:model=>model}, :layout => false if model.correct_predictions
- when "regression"
= haml :regression_validation, :locals=>{:model=>model}, :layout => false
- - else
- = image_tag("/snake_transparent.gif") if model.validation_status == "Running"
- %a{:href => model.validation_task_uri} #{model.validation_status}
-
+-# else
+ = image_tag("/snake_transparent.gif") if model.validation_status == "Running"
+ %a{:href => model.validation_task_uri} #{model.validation_status}
+