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require 'rubygems'
require 'compass' #must be loaded before sinatra
require 'sinatra'
require 'haml' #must be loaded after sinatra
require 'opentox-client'
require 'opentox-server'
require File.join(File.dirname(__FILE__),'helper.rb')
require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb")
helpers do
end
get '/?' do
redirect to('/predict')
end
get '/predict/?' do
@models = OpenTox::Model.all $model[:uri]
haml :predict
end
get '/jme_help/?' do
File.read(File.join('views','jme_help.html'))
end
# best way to get individual compound uri for details
get '/prediction/:neighbour/details/?' do
@compound_uri = OpenTox::Compound.new params[:neighbour]
@smiles = @compound_uri.smiles
task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "look for names.") do
names = @compound_uri.names
end
sleep 1
task.get
case task[RDF::OT.hasStatus]
when "Error"
@names = "There are no names for this compound available."
when "Completed"
@names = @compound_uri.names.join(",")
end
@inchi = @compound_uri.inchi.gsub("InChI=", "")
haml :details, :layout => false
end
post '/predict/?' do
# validate identifier input
task = OpenTox::Task.create($task[:uri], @subjectid, RDF::DC.description => "#{params[:identifier] ? params[:identifier] : "no valid SMILES string."}: Validate SMILES string.") do
# transfered input
@identifier = params[:identifier]
# get compound from SMILES
@compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s
# validate SMILES by converting to INCHI
inchi = @compound.inchi
end
# necessary to wait for task
sleep 1
task.get
$logger.debug "task uri: #{task.uri}"
$logger.debug "task status: #{task[RDF::OT.hasStatus]}"
# case task fails return message smiles invalid
# case task completed go ahead
case task[RDF::OT.hasStatus]
when "Error"
@error_report = "Not a valid SMILES string."
haml :error
when "Completed"
@identifier = params[:identifier]
@compound = OpenTox::Compound.from_smiles $compound[:uri], @identifier.to_s
# init
@@prediction_models = []
@@predictions = []
# init lazar algorithm
lazar = OpenTox::Algorithm.new File.join($algorithm[:uri],"lazar")
# gather models from service and compare if selected
params[:selection].each do |model|
@mselected = model[0]
@mall = OpenTox::Model.all $model[:uri]
@mall.each do |m|
m.get
@@prediction_models << m if m.title =~ /#{@mselected}/
end
$logger.debug "@prediction_models: #{@@prediction_models.inspect}"
end
# predict with selected models
# results in prediction variable
# store prediction in array for better handling
@@prediction_models.each do |m|
@prediction_uri = m.run :compound_uri => "#{@compound.uri}"
prediction = OpenTox::Dataset.new @prediction_uri
pa = []
pa << prediction
@@predictions << pa
end
haml :prediction
end
end
get '/stylesheets/:name.css' do
content_type 'text/css', :charset => 'utf-8'
sass(:"stylesheets/#{params[:name]}", Compass.sass_engine_options )
end
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