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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
task_uri = OpenTox::Task.as_task() do
LOGGER.info("Building nightly report")
benchmarks = [ HamsterTrainingTestBenchmark.new,
HamsterCrossvalidationBenchmark.new,
MiniRegressionBenchmark.new,
CacoModelsRegressionBenchmark.new,
CacoAlgsRegressionBenchmark.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
rescue => ex
LOGGER.error "uncaught nightly build error: "+ex.message
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
LOGGER.debug "Nighlty report, all benchmarks done "+running.inspect
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)
if (b.comparison_report)
report.add_table(section_results, b.comparison_report_title, [[b.comparison_report]], false)
end
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
if defined?(halt)
halt 202,task_uri
else
return task_uri
end
end
class AbstractBenchmark
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
def comparison_report_title
"algorithm comparison report"
end
def comparison_report
@comparison_report
end
end
class ValidationBenchmark < AbstractBenchmark
def info_table
raise "no comparables" unless @comparables
t = []
t << ["param", "uri"]
params.each do |k,v|
t << [k.to_s, v.to_s]
end
count = 1
@comparables.each do |alg|
t << [comparable_nice_name+" ["+count.to_s+"]", alg]
count += 1
end
t
end
def errors
@errors
end
def params
raise "return uri-value hash"
end
def validate(index)
raise "validate, return uri"
end
def build_report(index)
raise "build report, return uri"
end
def build_compare_report(comparables)
raise "build compare report, return uri"
end
def build()
raise "no comparables" unless @comparables
@validations = Array.new(@comparables.size)
@reports = Array.new(@comparables.size)
@errors = {}
to_compare = []
# 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: "+@comparables[i].to_s
@validations[i] = validate(i)
to_compare << @validations[i] if OpenTox::Utils.is_uri?(@validations[i])
begin
LOGGER.debug "Building validation-report for "+@validations[i].to_s+" ("+@comparables[i].to_s+")"
@reports[i] = build_report(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
if to_compare.size>1
LOGGER.debug self.class.to_s.gsub(/Nightly::/, "")+": build comparison report"
@comparison_report = build_compare_report(to_compare)
else
LOGGER.debug self.class.to_s.gsub(/Nightly::/, "")+": nothing to compare"
end
end
end
class AlgorithmValidationBenchmark < ValidationBenchmark
def comparable_nice_name
return "algorithm"
end
def build()
raise "no algs" unless @algs
@comparables = @algs
super
end
def build_compare_report(comparables)
Util.create_alg_comparison_report(comparables)
end
end
class ModelValidationBenchmark < ValidationBenchmark
def comparable_nice_name
return "model"
end
def build()
raise "no models" unless @models
@comparables = @models
super
end
def build_compare_report(comparables)
"model comparsion report not available yet" #Util.create_model_comparison_report(comparables)
end
end
class TestModelValidationBenchmark < ModelValidationBenchmark
def info
[ training_test_info ]
end
def training_test_info
"This is a test set validation of existing models. "+
"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 params
p = { "test_dataset_uri" => @test_data }
p["test_target_dataset_uri"] = @test_class_data if @test_class_data
return p
end
def validate(index)
Util.validate_model(@test_data, @test_class_data, @models[index])
end
def build_report(index)
Util.create_report(@validations[index])
end
def build()
raise "no test data" unless @test_data
super
end
end
class TrainingTestValidationBenchmark < AlgorithmValidationBenchmark
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 params
p = { "training_dataset_uri" => @train_data, "test_dataset_uri" => @test_data,
"prediction_feature" => @pred_feature }
p["test_target_dataset_uri"] = @test_class_data if @test_class_data
return p
end
def validate(index)
Util.validate_alg(@train_data, @test_data, @test_class_data,
@algs[index], @pred_feature, @alg_params[index])
end
def build_report(index)
Util.create_report(@validations[index])
end
def build()
raise "no train data" unless @train_data
raise "no test data" unless @test_data
raise "no pred feature" unless @pred_feature
super
end
end
class CrossValidationBenchmark < AlgorithmValidationBenchmark
def info
[ training_test_info ]
end
def training_test_info
"This is a cross-validation."
end
def info_table_title
"Cross-validation params"
end
def params
p = { "dataset_uri" => @data, "prediction_feature" => @pred_feature,
"num_folds" => @num_folds, "random_seed" => @random_seed, "stratified" => @stratified}
return p
end
def validate(index)
Util.cross_validate_alg(@data, @algs[index], @pred_feature,
@num_folds, @random_seed, @stratified, @alg_params[index])
end
def build_report(index)
Util.create_report(@validations[index], "crossvalidation")
end
def build()
raise "no data" unless @data
raise "no pred feature" unless @pred_feature
@num_folds = 10 unless @num_folds
@random_seed = 1 unless @random_seed
@stratified = false unless @stratified
super
end
end
class HamsterCrossvalidationBenchmark < CrossValidationBenchmark
@@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()
"Crossvalidation, binary classification"
end
def info
res = [ "A crossvalidation using the hamster carcinogenicity dataset." ] + super
return res
end
def build()
@algs = [
File.join(@@config[:services]["opentox-majority"],["/class/algorithm"]),
File.join(@@lazar_server,"lazar"),
"http://188.40.32.88/algorithm/lazar",
#File.join(@@config[:services]["opentox-majority"],["/class/algorithm"]),
#File.join(@@config[:services]["opentox-majority"],["/class/algorithm"]),
]
@alg_params = [
nil,
"feature_generation_uri="+File.join(@@lazar_server,"fminer"),
#"feature_generation_uri=http://188.40.32.88/algorithm/fminer",
nil,
nil
]
@pred_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
LOGGER.debug "upload hamster datasets"
@data = Util.upload_dataset(@@dataset_service, @@file, @@file_type).chomp("\n")
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(@@config[:services]["opentox-majority"],["/class/algorithm"]),
File.join(@@lazar_server,"lazar"),
"http://188.40.32.88/algorithm/lazar",
]
@alg_params = [
nil,
"feature_generation_uri="+File.join(@@lazar_server,"fminer"),
"feature_generation_uri=http://188.40.32.88/algorithm/fminer",
]
LOGGER.debug "prepare hamster datasets"
@pred_feature = "http://localhost/toxmodel/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
@test_class_data = Util.upload_dataset(@@dataset_service, @@file, @@file_type).chomp("\n")
#@pred_feature = "http://188.40.32.88/toxcreate/feature#Hamster%20Carcinogenicity%20(DSSTOX/CPDB)"
#@test_class_data = "http://188.40.32.88/dataset/57"
split = Util.split_dataset(@test_class_data, @pred_feature, 0.9, 1)
@train_data = split[0].to_s
@test_data = split[1].to_s
raise "could not split "+@train_data.to_s+" "+@test_data.to_s unless OpenTox::Utils.is_uri?(@train_data) and OpenTox::Utils.is_uri?(@test_data)
super
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.ntua.gr:3004/algorithm/mlr",
"http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/kNNregression",
File.join(@@config[:services]["opentox-majority"],["/regr/algorithm"])
]
@alg_params = [ nil, "dataset_service=http://ambit.uni-plovdiv.bg:8080/ambit2/dataset", 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 CacoAlgsRegressionBenchmark < TrainingTestValidationBenchmark
def title
"Training test set validation, regression, caco dataset"
end
def info
res = [ "Training test set validation on caco2 dataset." ] + super
return res
end
def build()
@algs = [
"http://opentox.ntua.gr:3003/algorithm/mlr",
"http://opentox.ntua.gr:3004/algorithm/mlr",
"http://ambit.uni-plovdiv.bg:8080/ambit2/algorithm/LR",
]
@alg_params = [ nil, nil]
@train_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R7798"
@test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R8353"
@pred_feature = "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/255510"
super
end
end
class CacoModelsRegressionBenchmark < TestModelValidationBenchmark
def title
"Regression model test set validation, caco dataset"
end
def info
res = [ "Valdation of two identical(?) mlr models on caco-2 dataset." ] + super
return res
end
def build()
@models = [
"http://ambit.uni-plovdiv.bg:8080/ambit2/model/259260",
"http://opentox.ntua.gr:3003/model/195",
]
#@test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R7798"
@test_data = "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/R8353"
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 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.to_s
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.to_s
end
def self.validate_model(test_data, test_class_data, model)
uri = OpenTox::RestClientWrapper.post @@validation_service, { :test_dataset_uri => test_data,
:test_target_dataset_uri => test_class_data, :model_uri => model }
return uri.to_s
end
def self.cross_validate_alg(data, alg, feature, folds, seed, stratified, alg_params)
uri = OpenTox::RestClientWrapper.post File.join(@@validation_service,"crossvalidation"), { :dataset_uri => data,
:algorithm_uri => alg, :prediction_feature => feature, :algorithm_params => alg_params, :num_folds => folds,
:random_seed => seed, :stratified => stratified }
#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.to_s
end
def self.create_report(validation, type="validation")
uri = OpenTox::RestClientWrapper.post File.join(@@validation_service,"report/"+type.to_s), { :validation_uris => validation }
#uri = OpenTox::Task.find(uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(uri)
return uri.to_s
end
def self.create_alg_comparison_report(validations)
uri = OpenTox::RestClientWrapper.post File.join(@@validation_service,"report/algorithm_comparison"), { :validation_uris => validations.join("\n") }
#uri = OpenTox::Task.find(uri).wait_for_resource.to_s if OpenTox::Utils.task_uri?(uri)
return uri.to_s
end
end
end
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