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require "rubygems"
require "sinatra"
before {
request.env['HTTP_HOST']="local-ot/algorithm"
request.env["REQUEST_URI"]=request.env["PATH_INFO"]
}
require "opentox-ruby"
ENV['RACK_ENV'] = 'test'
require 'application.rb'
require 'test/unit'
require 'rack/test'
LOGGER = Logger.new(STDOUT)
LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
module Sinatra
set :raise_errors, false
set :show_exceptions, false
module UrlForHelper
BASE = "http://local-ot/algorithm"
def url_for url_fragment, mode=:path_only
case mode
when :path_only
raise "not impl"
when :full
end
"#{BASE}#{url_fragment}"
end
end
end
class AlgorithmTest < Test::Unit::TestCase
include Rack::Test::Methods
def app
Sinatra::Application
end
def test_prediction
begin
#dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/603204?pagesize=100&page=0"
#test_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/603204?pagesize=100&page=1"
#feature_dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/603204?pagesize=200&page=0"
#prediction_feature = "http://apps.ideaconsult.net:8080/ambit2/feature/528321"
# dataset_uri = "http://apps.ideaconsult.net:8080/ambit2/dataset/425254"
# prediction_feature = "http://apps.ideaconsult.net:8080/ambit2/feature/528321"
##dataset_uri = "http://local-ot/dataset/1488"
#prediction_feature = "http://local-ot/dataset/1315/feature/Rodent%20carcinogenicity"
#kazius 250 no features
dataset_uri = "http://local-ot/dataset/9264"
prediction_feature = dataset_uri+"/feature/endpoint"
feature_dataset_uri = "http://local-ot/dataset/91409"
params = {:dataset_uri=>dataset_uri,
:prediction_feature=>prediction_feature,
:min_frequency=>7, :max_num_features=>300} #multi: 10=>4, 5=>>3000
# params = {:dataset_uri=>dataset_uri,
# :prediction_feature=>prediction_feature, :feature_dataset_uri=>feature_dataset_uri}
# post "/lazar",params
#post "/fminer/bbrc",params
#uri = wait_for_task(last_response.body)
#puts uri
#puts OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc"),params)
# model = uri
# puts "model #{model}"
# params = {:dataset_uri=>test_dataset_uri}
# puts OpenTox::RestClientWrapper.post(model,params)
#puts "features: "+OpenTox::Dataset.find(uri).features.size.to_s
feature_dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/3277"
dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/1333"
params = {:dataset_uri=>dataset_uri,
:feature_dataset_uri=>feature_dataset_uri}
#post "/fminer/bbrc/match",params
#uri = wait_for_task(last_response.body)
puts OpenTox::RestClientWrapper.post(File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/match"),params)
# puts uri
# fminer = File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
# OpenTox::RestClientWrapper.post(fminer,params)
# params = {:dataset_uri=>"http://local-ot/dataset/1488",
# :prediction_feature=>"http://local-ot/dataset/1315/feature/Rodent%20carcinogenicity",
# :min_frequency=>50}
# post "/lazar",params
# uri = wait_for_task(last_response.body)
# puts uri
#puts "features: "+OpenTox::Dataset.find(uri).features.size.to_s
# fminer = File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc")
# OpenTox::RestClientWrapper.post(fminer,params)
rescue => ex
rep = OpenTox::ErrorReport.create(ex, "")
puts rep.to_yaml
end
#get "/lazar",nil,'HTTP_ACCEPT' => "application/rdf+xml"
#get "/fminer",nil,'HTTP_ACCEPT' => "application/rdf+xml"
#OpenTox::Algorithm.Generic.find("http://localhost/algorithm/lazar")
# puts last_response.body
# webservice = "http://ot.algorithm.de/lazar"
# headers = {:dataset_uri=>"http://ot.dataset.de/2",
# :prediction_feature=>"http://localhost/toxmodel/feature%23Hamster%20Carcinogenicity%20(DSSTOX/CPDB)",
# :feature_generation_uri=>"http://ot.algorithm.de/fminer"}
#
# #puts OpenTox::RestClientWrapper.post(webservice,headers)
# post webservice,headers
# #puts
# uri = wait_for_task(last_response.body.to_s)
# puts uri
# puts OpenTox::RestClientWrapper.get(uri,:accept => 'application/rdf+xml')
# #get uri
end
# see test_util.rb
def wait_for_task(uri)
if uri.task_uri?
task = OpenTox::Task.find(uri)
task.wait_for_completion
raise "task failed: "+uri.to_s if task.error?
uri = task.result_uri
end
return uri
end
end
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