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require_relative "setup.rb"
test_path = File.expand_path(File.dirname(__FILE__))
require File.join(test_path,"validation_util.rb")
begin
puts "Service URI is: #{$validation[:uri]}"
rescue
puts "Configuration Error: $validation[:uri] is not defined in: " + File.join(ENV["HOME"],".opentox","config","test.rb")
exit
end
DELETE = true
TEST_LISTS = false
DATA = []
#DATA << { :type => :crossvalidation,
# :data => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?max=100",
# :feat => "http://apps.ideaconsult.net:8080/ambit2/feature/26221",
# :info => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?max=100" }
# DATA << { :type => :training_test_validation,
# :train_data => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?page=0&pagesize=150",
# :test_data => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?page=3&pagesize=50",
# :feat => "http://apps.ideaconsult.net:8080/ambit2/feature/26221",
# :info => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?page=0&pagesize=150" }
# DATA << { :type => :training_test_validation,
# :train_data => "http://apps.ideaconsult.net:8080/ambit2/dataset/435293?page=0&pagesize=300",
# :test_data => "http://apps.ideaconsult.net:8080/ambit2/dataset/435293?page=30&pagesize=10",
# :feat => "http://apps.ideaconsult.net:8080/ambit2/feature/533748",
# :info => "http://apps.ideaconsult.net:8080/ambit2/dataset/435293?page=0&pagesize=300" }
FILES = {
File.new(File.join(test_path,"data","hamster_carcinogenicity.csv")) => :split_validation,
File.new(File.join(test_path,"data","EPAFHM.medi.csv")) => :split_validation,
}
unless defined?($short_tests)
FILES.merge!({
File.new(File.join(test_path,"data","hamster_carcinogenicity.csv")) => :crossvalidation,
File.new("data/EPAFHM.medi.csv") => :crossvalidation,
# File.new("data/hamster_carcinogenicity.csv") => :bootstrap_validation
})
end
FEAT_GEN = {}
FILES.each do |f,t|
if f.path=~/hamster/
FEAT_GEN[f] = [ File.join($algorithm[:uri],"fminer/bbrc") ] #FEAT_GEN[f] << File.join($algorithm[:uri],"fminer/last")
elsif f.path=~/EPAFHM/
FEAT_GEN[f] = [ File.join($algorithm[:uri],"descriptor","physchem") ]
else
raise "please define feature generation uri for dataset: #{f.path}"
end
end
class ValidationTest < MiniTest::Test
i_suck_and_my_tests_are_order_dependent!
def global_setup
# subjectid is set in setup.rb
puts "login and upload datasets"
OpenTox::RestClientWrapper.subjectid ? puts("logged in: "+OpenTox::RestClientWrapper.subjectid.to_s) : puts("AA disabled")
FILES.each do |file,type|
data = { :type => type,
:data => ValidationTestUtil.upload_dataset(file),
:feat => ValidationTestUtil.prediction_feature_for_file(file),
:split_ratio => (file.path=~/EPAFHM/ ? 0.95 : 0.9),#only used for split_validation
:info => file.path, :delete => true}
FEAT_GEN[file].each do |feat_gen|
data[:alg_params] = "feature_generation_uri="+feat_gen
data[:alg_params] << ";backbone=false;min_chisq_significance=0.0" if feat_gen=~/fminer/ and data[:info] =~ /mini/
if feat_gen=~/physchem/
# validation with physchem descriptors is performed twice, once with feature_generation_uri, once with feature_dataset_uri
desc = [ "Openbabel.atoms", "Openbabel.bonds", "Openbabel.dbonds", "Openbabel.HBA1", "Openbabel.HBA2", "Openbabel.HBD", "Openbabel.MP", "Openbabel.MR", "Openbabel.MW", "Openbabel.nF", "Openbabel.sbonds", "Openbabel.tbonds", "Openbabel.TPSA"]
data[:alg_params] << ";descriptors="+desc.join(",")
DATA << data
feature_dataset_uri = OpenTox::Algorithm::Generic.new(feat_gen).run({:dataset_uri => data[:data], :descriptors => desc})
data[:alg_params] = "feature_dataset_uri="+feature_dataset_uri
DATA << data
else
DATA << data
end
end
end
end
def global_teardown
puts "delete and logout"
if defined?(DELETE) and DELETE
[:data, :train_data, :test_data].each do |d|
DATA.each do |data|
OpenTox::Dataset.new(data[d]).delete if data[d] and data[:delete]
end
end
@@vs.each{|v| v.delete} if defined?@@vs
@@cvs.each{|cv| cv.delete} if defined?@@cvs
@@reports.each{|report| report.delete} if defined?@@reports
end
end
def test_validation_list
return unless TEST_LISTS
puts "test_validation_list"
list = OpenTox::Validation.list
assert list.is_a?(Array)
list.each do |l|
assert l.uri?
end
end
def test_bootstrapping
@@vs = [] unless defined?@@vs
DATA.each do |data|
if data[:type]==:bootstrap_validation
puts "bootstrapping "+data[:info].to_s
p = {
:dataset_uri => data[:data],
:algorithm_uri => File.join($algorithm[:uri],"lazar"),
:algorithm_params => data[:alg_params],
:prediction_feature => data[:feat],
:random_seed => 2}
t = OpenTox::SubTask.new(nil,0,1)
def t.progress(pct)
if !defined?@last_msg or @last_msg+10<Time.new
puts "waiting for boostrap validation: "+pct.to_s
@last_msg=Time.new
end
end
def t.waiting_for(task_uri); end
v = OpenTox::Validation.create_bootstrapping_validation(p, t)
assert v.uri.uri?
if $aa[:uri]
assert_unauthorized do
OpenTox::Validation.find(v.uri)
end
end
v = OpenTox::Validation.find(v.uri)
assert_valid_date v
assert v.uri.uri?
assert_prob_correct(v)
model = v.metadata[RDF::OT.model.to_s]
assert model.uri?
v_list = OpenTox::Validation.list( {:model => model} )
assert v_list.size==1 and v_list.include?(v.uri)
puts v.uri unless defined?(DELETE) and DELETE
@@vs << v
end
end
end
def test_training_test_split
@@vs = [] unless defined?@@vs
DATA.each do |data|
if data[:type]==:split_validation
puts "test_training_test_split "+data[:info].to_s
p = {
:dataset_uri => data[:data],
:algorithm_uri => File.join($algorithm[:uri],"lazar"),
:algorithm_params => data[:alg_params],
:prediction_feature => data[:feat],
:split_ratio => data[:split_ratio],
:random_seed => 2}
t = OpenTox::SubTask.new(nil,0,1)
def t.progress(pct)
if !defined?@last_msg or @last_msg+10<Time.new
puts "waiting for training-test-split validation: "+pct.to_s
@last_msg=Time.new
end
end
def t.waiting_for(task_uri); end
v = OpenTox::Validation.create_training_test_split(p, t)
assert v.uri.uri?
if $aa[:uri]
assert_unauthorized do
OpenTox::Validation.find(v.uri)
end
end
v = OpenTox::Validation.find(v.uri)
#v_uri = "http://localhost:8087/validation/90"
#v = OpenTox::Validation.find(v_uri)
assert_valid_date v
assert v.uri.uri?
assert_prob_correct(v)
train_compounds = OpenTox::Dataset.find(v.metadata[RDF::OT.trainingDataset.to_s]).compounds
test_compounds = OpenTox::Dataset.find(v.metadata[RDF::OT.testDataset.to_s]).compounds
orig_compounds = OpenTox::Dataset.find(data[:data]).compounds
assert_equal((orig_compounds.size*data[:split_ratio]).round,train_compounds.size)
assert_equal(orig_compounds.size,(train_compounds+test_compounds).size)
assert_equal(orig_compounds.uniq.size,(train_compounds+test_compounds).uniq.size)
model = v.metadata[RDF::OT.model.to_s]
assert model.uri?
v_list = OpenTox::Validation.list( {:model => model} )
assert v_list.size==1 and v_list.include?(v.uri)
puts v.uri unless defined?(DELETE) and DELETE
@@vs << v
end
end
end
def test_training_test_validation
@@vs = [] unless defined?@@vs
DATA.each do |data|
if data[:type]==:training_test_validation
puts "test_training_test_validation "+data[:info].to_s
p = {
:training_dataset_uri => data[:train_data],
:test_dataset_uri => data[:test_data],
:algorithm_uri => File.join($algorithm[:uri],"lazar"),
:algorithm_params => data[:alg_params],
:prediction_feature => data[:feat]}
t = OpenTox::SubTask.new(nil,0,1)
def t.progress(pct)
if !defined?@last_msg or @last_msg+10<Time.new
puts "waiting for training-test-set validation: "+pct.to_s
@last_msg=Time.new
end
end
def t.waiting_for(task_uri); end
v = OpenTox::Validation.create_training_test_validation(p, t)
assert v.uri.uri?
if $aa[:uri]
assert_unauthorized do
OpenTox::Validation.find(v.uri)
end
end
v = OpenTox::Validation.find(v.uri)
assert_valid_date v
assert v.uri.uri?
assert_prob_correct(v)
model = v.metadata[RDF::OT.model.to_s]
assert model.uri?
v_list = OpenTox::Validation.list( {:model => model} )
assert v_list.size==1 and v_list.include?(v.uri)
puts v.uri unless defined?(DELETE) and DELETE
@@vs << v
end
end
end
def test_filter_predictions
(@@vs + @@cv).each do |v|
v = v.statistics if v.is_a?(OpenTox::Crossvalidation)
puts v.metadata.to_yaml
assert v.metadata[RDF::OT.numInstances.to_s].to_i>3
# get top 3 predictions
filtered = v.filter(nil, nil, 3)
puts filtered.to_yaml
assert filtered[RDF::OT.numInstances.to_s].to_i==3,"#{filtered[RDF::OT.numInstances.to_s]} != 3"
assert filtered[RDF::OT.numUnpredicted.to_s].to_i==0
# get predictions with min confidence 0.5 but at least 5 predictions
filtered = v.filter(0.5, 5)
puts filtered.to_yaml
assert filtered[RDF::OT.numInstances.to_s].to_i>=5
end
end
def test_validation_report
@@reports = [] unless defined?@@reports
@@vs.each do |v|
puts "test_validation_report"
assert defined?v,"no validation defined"
assert_kind_of OpenTox::Validation,v
if $aa[:uri]
assert_unauthorized do
OpenTox::ValidationReport.create(v.uri)
end
end
report = OpenTox::ValidationReport.find_for_validation(v.uri)
assert_nil report,"report already exists for validation\nreport: "+(report ? report.uri.to_s : "")+"\nvalidation: "+v.uri.to_s
params = {:min_confidence => 0.05}
report = OpenTox::ValidationReport.create(v.uri,params)
assert report.uri.uri?
if $aa[:uri]
assert_unauthorized do
OpenTox::ValidationReport.find(report.uri)
end
end
report = OpenTox::ValidationReport.find(report.uri)
assert_valid_date report
assert report.uri.uri?
report2 = OpenTox::ValidationReport.find_for_validation(v.uri)
assert_equal report.uri,report2.uri
report3_uri = v.find_or_create_report
assert_equal report.uri,report3_uri
puts report2.uri unless defined?(DELETE) and DELETE
@@reports << report2
end
end
def test_crossvalidation_list
return unless TEST_LISTS
puts "test_crossvalidation_list"
list = OpenTox::Crossvalidation.list
assert list.is_a?(Array)
list.each do |l|
assert l.uri?
end
end
def test_crossvalidation
#assert_rest_call_error OpenTox::NotFoundError do
# OpenTox::Crossvalidation.find(File.join(CONFIG[:services]["opentox-validation"],"crossvalidation/noexistingid"))
#end
@@cvs = []
@@cv_datasets = []
@@cv_identifiers = []
DATA.each do |data|
if data[:type]==:crossvalidation
puts "test_crossvalidation "+data[:info].to_s+" "+data[:alg_params]
p = {
:dataset_uri => data[:data],
:algorithm_uri => File.join($algorithm[:uri],"lazar"),
:algorithm_params => data[:alg_params],
:prediction_feature => data[:feat],
:num_folds => 10 }
#:num_folds => 2 }
t = OpenTox::SubTask.new(nil,0,1)
def t.progress(pct)
if !defined?@last_msg or @last_msg+10<Time.new
puts "waiting for crossvalidation: "+pct.to_s
@last_msg=Time.new
end
end
def t.waiting_for(task_uri); end
cv = OpenTox::Crossvalidation.create(p, t)
assert cv.uri.uri?
if $aa[:uri]
assert_unauthorized do
OpenTox::Crossvalidation.find(cv.uri)
end
end
cv = OpenTox::Crossvalidation.find(cv.uri)
assert_valid_date cv
assert cv.uri.uri?
stats_val = cv.statistics
assert_kind_of OpenTox::Validation,stats_val
assert_prob_correct(stats_val)
algorithm = cv.metadata[RDF::OT.algorithm.to_s]
assert algorithm.uri?
cv_list = OpenTox::Crossvalidation.list( {:algorithm => algorithm} )
assert cv_list.include?(cv.uri)
cv_list.each do |cv_uri|
#begin catch not authorized somehow
alg = OpenTox::Crossvalidation.find(cv_uri).metadata[RDF::OT.algorithm.to_s]
assert alg==algorithm,"wrong algorithm for filtered crossvalidation, should be: '"+algorithm.to_s+"', is: '"+alg.to_s+"'"
#rescue
#end
end
puts cv.uri unless defined?(DELETE) and DELETE
@@cvs << cv
@@cv_datasets << data
@@cv_identifiers << data[:alg_params]
end
end
end
def test_crossvalidation_report
#@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/48", SUBJECTID)
@@reports = [] unless defined?@@reports
@@cvs.each do |cv|
puts "test_crossvalidation_report"
assert defined?cv,"no crossvalidation defined"
assert_kind_of OpenTox::Crossvalidation,cv
#assert_rest_call_error OpenTox::NotFoundError do
# OpenTox::CrossvalidationReport.find_for_crossvalidation(cv.uri)
#end
if $aa[:uri]
assert_unauthorized do
OpenTox::CrossvalidationReport.create(cv.uri)
end
end
assert OpenTox::CrossvalidationReport.find_for_crossvalidation(cv.uri)==nil
report = OpenTox::CrossvalidationReport.create(cv.uri)
assert report.uri.uri?
if $aa[:uri]
assert_unauthorized do
OpenTox::CrossvalidationReport.find(report.uri)
end
end
report = OpenTox::CrossvalidationReport.find(report.uri)
assert_valid_date report
assert report.uri.uri?
report2 = OpenTox::CrossvalidationReport.find_for_crossvalidation(cv.uri)
assert_equal report.uri,report2.uri
report3_uri = cv.find_or_create_report
assert_equal report.uri,report3_uri
puts report2.uri unless defined?(DELETE) and DELETE
@@reports << report2
end
end
def test_crossvalidation_compare_report
@@reports = [] unless defined?@@reports
@@cvs.size.times do |i|
@@cvs.size.times do |j|
if j>i and @@cv_datasets[i]==@@cv_datasets[j]
puts "test_crossvalidation_compare_report"
assert_kind_of OpenTox::Crossvalidation,@@cvs[i]
assert_kind_of OpenTox::Crossvalidation,@@cvs[j]
hash = { @@cv_identifiers[i] => [@@cvs[i].uri],
@@cv_identifiers[j] => [@@cvs[j].uri] }
if $aa[:uri]
assert_unauthorized do
OpenTox::AlgorithmComparisonReport.create hash,{}
end
end
assert OpenTox::AlgorithmComparisonReport.find_for_crossvalidation(@@cvs[i].uri)==nil
assert OpenTox::AlgorithmComparisonReport.find_for_crossvalidation(@@cvs[j].uri)==nil
params = {:ttest_significance => 0.95, :ttest_attributes => "real_runtime,percent_unpredicted", :max_num_predictions => 5}
report = OpenTox::AlgorithmComparisonReport.create hash,params
assert report.uri.uri?
if $aa[:uri]
assert_unauthorized do
OpenTox::AlgorithmComparisonReport.find(report.uri)
end
end
report = OpenTox::AlgorithmComparisonReport.find(report.uri)
assert_valid_date report
assert report.uri.uri?
report2 = OpenTox::AlgorithmComparisonReport.find_for_crossvalidation(@@cvs[i].uri)
assert_equal report.uri,report2.uri
report3 = OpenTox::AlgorithmComparisonReport.find_for_crossvalidation(@@cvs[j].uri)
assert_equal report.uri,report3.uri
puts report2.uri unless defined?(DELETE) and DELETE
@@reports << report2
end
end
end
end
# checks if opentox_object has date defined in metadata, and time is less than max_time seconds ago
def assert_valid_date( opentox_object, max_time=600 )
internal_server_error "no opentox object" unless opentox_object.class.to_s.split("::").first=="OpenTox"
assert opentox_object.metadata.is_a?(Hash)
puts opentox_object.class
puts RDF::DC.date.to_s
puts opentox_object.metadata.inspect
assert opentox_object.metadata[RDF::DC.date.to_s],"date not set for "+opentox_object.uri.to_s+", is metadata loaded? (use find) :\n"+opentox_object.metadata.to_yaml
time = Time.parse(opentox_object.metadata[RDF::DC.date.to_s])
assert time!=nil
=begin
assert time<Time.new,"date of "+opentox_object.uri.to_s+" is in the future: "+time.to_s
assert time>Time.new-(10*60),opentox_object.uri.to_s+" took longer than 10 minutes "+time.to_s
=end
end
def assert_prob_correct( validation )
class_stats = validation.metadata[RDF::OT.classificationStatistics]
if class_stats != nil
class_value_stats = class_stats[RDF::OT.classValueStatistics]
class_value_stats.each do |cs|
#puts cs[RDF::OT.positivePredictiveValue]
#puts validation.probabilities(0,cs[RDF::OT.classValue]).inspect
assert cs[RDF::OT.positivePredictiveValue]==validation.probabilities(0,cs[RDF::OT.classValue])[:probs][cs[RDF::OT.classValue]]
end
end
end
def assert_unauthorized
unless $aa[:uri]
puts "AA disabled: skipping test for not authorized"
return
else
subjectid = OpenTox::RestClientWrapper.subjectid
OpenTox::RestClientWrapper.subjectid = nil
begin
res = yield
assert false,"no un-authorized error thrown, result is #{res}"
rescue => ex
assert ex.is_a?(OpenTox::UnauthorizedError),"not unauthorized error, instead: #{ex.class}"
ensure
OpenTox::RestClientWrapper.subjectid = subjectid
end
end
end
# hack to have a global_setup and global_teardown
def teardown
if((@@expected_test_count-=1) == 0)
global_teardown
end
end
def setup
unless defined?@@expected_test_count
@@expected_test_count = (self.class.instance_methods.reject{|method| method[0..3] != 'test'}).length
global_setup
end
end
end
|