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|
['rubygems', "haml", "sass", "rack-flash"].each do |lib|
require lib
end
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')
use Rack::Session::Cookie, :expire_after => 28800,
:secret => "ui6vaiNi-change_me"
use Rack::Flash
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 OpenTox::RestClientWrapper.put(File.join(model.task_uri, "Cancelled"), "Cancelled",{:subjectid => 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)
if model.training_dataset
delete_dependent(model.training_dataset, subjectid) if model.training_dataset.match(CONFIG[:services]["opentox-dataset"])
end
task.progress(90)
if model.feature_dataset
delete_dependent(model.feature_dataset, subjectid) if model.feature_dataset.match(CONFIG[:services]["opentox-dataset"])
end
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')
end
get '/login' do
haml :login
end
get '/models/?' do
@models = ToxCreateModel.all.sort(:order => "DESC")
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
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
put '/model/:id/?' do
response['Content-Type'] = 'text/plain'
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
case params[:view]
when "model"
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
get '/predict/?' do
@models = ToxCreateModel.all.sort(:order => "DESC")
@models = @models.collect{|m| m if m.status == 'Completed'}.compact
haml :predict
end
get '/create' do
haml :create
end
get '/help' do
haml :help
end
get "/confidence" do
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
get '/echa' do
@endpoints = OpenTox::Ontology::Echa.endpoints
haml :echa
end
post '/ambit' do
session[:echa] = params[:endpoint]
@datasets = OpenTox::Ontology::Echa.datasets(params[:endpoint])
haml :ambit
end
post '/feature' do
session[:dataset] = params[:dataset]
@features = []
OpenTox::Dataset.new(params[:dataset]).load_features.each do |uri,metadata|
@features << OpenTox::Feature.find(uri, @subjectid) if metadata[OWL.sameAs].match(/#{session[:echa]}/)
end
haml :feature
end
post '/models' do # create a new model
unless (params[:dataset] and params[:prediction_feature]) or (params[:file] and params[:file][:tempfile]) #params[:endpoint] and
flash[:notice] = "Please upload a Excel or CSV file or select an AMBIT dataset."
redirect url_for('/create')
end
unless logged_in()
logout
flash[:notice] = "Please login to create a new model."
redirect url_for('/create')
end
subjectid = session[:subjectid] ? session[:subjectid] : nil
if params[:dataset] and params[:prediction_feature]
@dataset = OpenTox::Dataset.new(params[:dataset],subjectid)
name = @dataset.load_metadata[DC.title]
@prediction_feature = OpenTox::Feature.find params[:prediction_feature], subjectid
@dataset.load_compounds
elsif params[:file][:filename]
name = params[:file][:filename].sub(/\..*$/,"")
end
@model = ToxCreateModel.create(:name => name, :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|
task.progress(5)
@model.update :status => "Uploading and saving dataset", :task_uri => task.uri
unless params[:dataset] and params[:prediction_feature]
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"
excel_file = params[:file][:tempfile].path + File.extname(params[:file][:filename])
File.rename(params[:file][:tempfile].path, excel_file) # add extension, spreadsheet does not read files without extensions
@dataset.load_spreadsheet(Excel.new excel_file, subjectid)
if @dataset.metadata[OT.Errors]
error "Incorrect file format. Please follow the instructions for #{link_to "Excel", "/help"} or #{link_to "CSV", "/help"} formats."
end
else
error "#{params[:file][:filename]} has a unsupported file type."
end
@dataset.save(subjectid)
rescue => e
error "Dataset creation failed with #{e.message}"
end
if @dataset.features.keys.size != 1
error "More than one feature in dataset #{params[:file][:filename]}. Please delete irrelvant columns and try again."
else
@prediction_feature = OpenTox::Feature.find(@dataset.features.keys.first,subjectid)
end
end
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", "/help"}? 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
@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] and @dataset.metadata[OT.Warnings].empty?
task.progress(15)
begin
lazar = OpenTox::Model::Lazar.create(:dataset_uri => @dataset.uri, :prediction_feature => @prediction_feature.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", "/help"} or #{link_to "CSV", "/help"} format."
end
task.progress(25)
=begin
type = "unknown"
if lazar.metadata[RDF.type].grep(/Classification/)
type = "classification"
elsif lazar.metadata[RDF.type].grep(/Regression/)
type = "regression"
end
=end
@model.update :type => @prediction_feature.feature_type, :feature_dataset => lazar.metadata[OT.featureDataset], :uri => lazar.uri
if CONFIG[:services]["opentox-validation"]
@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}"
# create summary
validation.summary(subjectid).each do |k,v|
begin
eval "@model.update :#{k.to_s} => v" if v
rescue
eval "@model.update :#{k.to_s} => 0"
end
end
@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
else
@model.update(:status => "Completed") #, :warnings => @model.warnings + "\nValidation service cannot be accessed from localhost.")
task.progress(100)
end
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')
end
post '/predict/?' do # post chemical name to model
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, subjectid)
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]
lazar = OpenTox::Model::Lazar.new @model_uri
prediction_dataset_uri = lazar.run(:compound_uri => params[:compound_uri], :subjectid => session[: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
flash[:notice] = "Login failed. Please try again."
haml :login
end
end
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.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
get '/stylesheets/style.css' do
headers 'Content-Type' => 'text/css; charset=utf-8'
sass :style
end
|