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class Nightly
NIGHTLY_REP_DIR = File.join(FileUtils.pwd,"nightly")
NIGHTLY_REPORT_XML = "nightly_report.xml"
NIGHTLY_REPORT_HTML = "nightly_report.html"
def self.get_nightly
LOGGER.info("Accessing nightly report.")
if File.exist?(File.join(NIGHTLY_REP_DIR,NIGHTLY_REPORT_HTML))
return File.new(File.join(NIGHTLY_REP_DIR,NIGHTLY_REPORT_HTML))
else
return "Nightly report not available, try again later"
end
end
def self.build_nightly
OpenTox::Task.as_task do
LOGGER.info("Building nightly report")
benchmarks = [ HamsterTrainingTestBenchmark.new,
MiniRegressionBenchmark.new,
FatheadRegressionBenchmark.new,
]
running = []
report = Reports::XMLReport.new("Nightly Validation", Time.now.strftime("Created at %m.%d.%Y - %H:%M"))
benchmarks.each do |b|
running << b.class.to_s.gsub(/Nightly::/, "")+b.object_id.to_s
Thread.new do
begin
b.build
ensure
running.delete(b.class.to_s.gsub(/Nightly::/, "")+b.object_id.to_s)
end
end
end
wait = 0
while running.size>0
LOGGER.debug "Nighlty report waiting for "+running.inspect if wait%60==0
wait += 1
sleep 1
end
section_about = report.add_section(report.get_root_element, "About this report")
report.add_paragraph(section_about,
"This a opentox internal test report. Its purpose is to maintain interoperability between the OT validation web service "+
"and other OT web services. If you have any comments, remarks, or wish your service/test-case to be added, please email "+
"to guetlein@informatik.uni-freiburg.de or use the issue tracker at http://opentox.informatik.uni-freiburg.de/simple_ot_stylesheet.css")
benchmarks.each do |b|
section = report.add_section(report.get_root_element, b.title)
section_info = report.add_section(section, "Info")
b.info.each{|i| report.add_paragraph(section_info,i)}
info_table = b.info_table
report.add_table(section_info, b.info_table_title, info_table) if info_table
section_results = report.add_section(section, "Results")
report.add_table(section_results, b.result_table_title, b.result_table)
section_errors = report.add_section(section, "Errors")
if b.errors and b.errors.size>0
b.errors.each do |k,v|
elem = report.add_section(section_errors,k)
report.add_paragraph(elem,v,true)
end
else
report.add_paragraph(section_errors,"no errors occured")
end
end
report.write_to(File.new(File.join(NIGHTLY_REP_DIR,NIGHTLY_REPORT_XML), "w"))
Reports::ReportFormat.format_report_to_html(NIGHTLY_REP_DIR,
NIGHTLY_REPORT_XML,
NIGHTLY_REPORT_HTML,
nil)
#"http://www.opentox.org/portal_css/Opentox%20Theme/base-cachekey7442.css")
#"http://apps.ideaconsult.net:8080/ToxPredict/style/global.css")
LOGGER.info("Nightly report completed")
return "Nightly report completed"
end
end
class ValidationBenchmark
def info_table_title
return title
end
def info_table
return nil
end
def result_table_title
return "Validation results"
end
def result_table
raise "no comparables" unless @comparables
raise "no validations" unless @validations
raise "no reports" unless @reports
t = []
row = [comparable_nice_name, "validation", "report"]
t << row
(0..@comparables.size-1).each do |i|
row = [ @comparables[i], @validations[i], @reports[i] ]
t << row
end
t
end
end
class TrainingTestValidationBenchmark < ValidationBenchmark
def info
[ training_test_info ]
end
def training_test_info
"This is a training test set validation. It builds a model with an algorithm and the training dataset. "+
"The model is used to predict the test dataset. Evaluation is done by comparing the model predictions "+
"to the actual test values (in the test target dataset)."
end
def info_table_title
"Validation params"
end
def comparable_nice_name
return "algorithm"
end
def info_table
t = []
t << ["param", "uri"]
t << ["training_dataset_uri", @train_data]
t << ["test_dataset_uri", @test_data]
t << ["test_target_dataset_uri", @test_class_data] if @test_class_data
t << ["prediction_feature", @pred_feature]
count = 1
@algs.each do |alg|
t << ["algorithm_uri"+" ["+count.to_s+"]", alg]
count += 1
end
t
end
def errors
@errors
end
def build()
raise "no algs" unless @algs
raise "no train data" unless @train_data
raise "no test data" unless @test_data
raise "no pred feature" unless @pred_feature
@comparables = @algs
@validations = Array.new(@comparables.size)
@reports = Array.new(@comparables.size)
@errors = {}
# LOGGER.info "train-data: "+@train_data.to_s
# LOGGER.info "test-data: "+@test_data.to_s
# LOGGER.info "test-class-data: "+@test_class_data.to_s
running = []
(0..@comparables.size-1).each do |i|
Thread.new do
running << @comparables[i]+i.to_s
begin
LOGGER.debug "Validate: "+@algs[i].to_s
@validations[i] = Util.validate_alg(@train_data, @test_data, @test_class_data,
@algs[i], URI.decode(@pred_feature), @alg_params[i]).to_s
begin
LOGGER.debug "Building validation-report for "+@validations[i].to_s+" ("+@algs[i].to_s+")"
@reports[i] = Util.create_report(@validations[i])
rescue => ex
LOGGER.error "validation-report error: "+ex.message
@reports[i] = "error"
end
rescue => ex
LOGGER.error "validation error: "+ex.message
key = "Error validating "+@comparables[i].to_s
@validations[i] = key+" (see below)"
@errors[key] = ex.message
ensure
running.delete(@comparables[i]+i.to_s)
end
end
end
wait = 0
while running.size>0
LOGGER.debug self.class.to_s.gsub(/Nightly::/, "")+" waiting for "+running.inspect if wait%20==0
wait += 1
sleep 1
end
end
end
class MiniRegressionBenchmark < TrainingTestValidationBenchmark
def title
"Training test set validation, small regression dataset"
end
def info
res = [ "A very small regression task, using the training dataset as test set." ] + super
return res
end
def build()
@algs = [ "http://opentox.ntua.gr:3003/algorithm/mlr",
"http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/kNNregression"
]
@alg_params = [nil, nil]
@train_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/342"
@test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/342"
@pred_feature = "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/103141"
super
end
end
class FatheadRegressionBenchmark < TrainingTestValidationBenchmark
def title
"Training test set validation, regression with fathead minnow dataset"
end
def info
res = [ "This is the regression use case used in D2.2. "+
"The task is to predict LC50 values of the well known Fathead Minnow Acute Toxicity dataset. "+
"JOELIB was used to compute numerical descriptors as features." ] + super
return res
end
def build()
@algs = [
"http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/kNNregression",
"http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/M5P",
"http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/GaussP"
]
@alg_params = [nil, nil, nil]
@train_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/639"
@test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/640"
@pred_feature = "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/264185"
super
end
end
class HamsterTrainingTestBenchmark < TrainingTestValidationBenchmark
@@dataset_service = @@config[:services]["opentox-dataset"]
@@file=File.new("data/hamster_carcinogenicity.yaml","r")
@@file_type="text/x-yaml"
@@lazar_server = @@config[:services]["opentox-algorithm"]
def title()
"Training test set validation, binary classification"
end
def info
res = [ "A simple binary classification task using the hamster carcinogenicity dataset." ] + super
return res
end
def build()
@algs = [File.join(@@lazar_server,"lazar")]
@alg_params = ["feature_generation_uri="+File.join(@@lazar_server,"fminer")]
@pred_feature = "http://localhost/toxmodel/feature%23Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
LOGGER.debug "pepare hamster datasets"
@test_class_data = Util.upload_dataset(@@dataset_service, @@file, @@file_type).chomp("\n")
split = Util.split_dataset(@test_class_data, URI.decode(@pred_feature), 0.9, 1)
@train_data = split[0].to_s
@test_data = split[1].to_s
super
end
end
class Util
@@validation_service = @@config[:services]["opentox-validation"]
def self.upload_dataset(dataset_service, file, file_type)
raise "File not found: "+file.path.to_s unless File.exist?(file.path)
data = File.read(file.path)
data_uri = OpenTox::RestClientWrapper.post dataset_service, {:content_type => file_type}, data
#data_uri = OpenTox::Task.find(data_uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(data_uri)
return data_uri
end
def self.split_dataset(data_uri, feature, split_ratio, random_seed)
res = OpenTox::RestClientWrapper.post File.join(@@validation_service,'plain_training_test_split'), { :dataset_uri => data_uri, :prediction_feature=>feature, :split_ratio=>split_ratio, :random_seed=>random_seed}
return res.split("\n")
end
def self.validate_alg(train_data, test_data, test_class_data, alg, feature, alg_params)
uri = OpenTox::RestClientWrapper.post @@validation_service, { :training_dataset_uri => train_data, :test_dataset_uri => test_data,
:test_target_dataset_uri => test_class_data,
:algorithm_uri => alg, :prediction_feature => feature, :algorithm_params => alg_params }
#LOGGER.info "waiting for validation "+uri.to_s
#uri = OpenTox::Task.find(uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(uri)
#LOGGER.info "validaiton done "+uri.to_s
return uri
end
def self.create_report(validation)
uri = OpenTox::RestClientWrapper.post File.join(@@validation_service,"report/validation"), { :validation_uris => validation }
#uri = OpenTox::Task.find(uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(uri)
return uri
end
end
end
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